GEMINI

GEMINI COMBO
Compact Microplate Processor

Assay Programming Manual

Edition: Date: February 2016
Part No.: 15100009588
Revision: 6

Software: GEMINI / GEMINI COMBO: User Software from Version 2.03

Original Document

We reserve the right to make changes in the course of technical development

without previous notice.

Copyright © 2016, STRATEC Biomedical AG. All rights reserved.

STRATEC Biomedical AG
Gewerbestraße 37
75217 Birkenfeld, GERMANY

Neither this manual nor any parts of it may be duplicated or transmitted in any way without the written
approval of STRATEC Biomedical AG.
Table of Contents

1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
1.1 Typographical Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
1.1.1 Display of Warnings and Notes. . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
1.1.2 Used Warning Symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
1.1.3 Special Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-3
1.2 Safety Instructions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4
1.2.1 General Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4
1.2.2 Electrical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-6
1.2.3 Laser Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-7
1.2.4 Mechanical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-8
1.2.5 Biological Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-9

2 Assay Programming . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1

2.1 Introduction and Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
2.1.1 Defining a New Assay. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
2.1.2 Defining Assay Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-7
2.1.3 Editing Existing Assays. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-9
2.1.4 Basic Structure of Assay Files . . . . . . . . . . . . . . . . . . . . . . . . . 2-10
2.1.5 Password Protection for Assays . . . . . . . . . . . . . . . . . . . . . . . . 2-11
2.2 Assay Protocol Header Information. . . . . . . . . . . . . . . . . . . . . . 2-12
2.2.1 Creating Plate Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-15
2.2.2 Dynamic Barcodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-16
2.3 Assay Layout Definition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-18
2.3.1 As s a y La y ou t Dialog Function Overview . . . . . . . . . . . . . 2-18
2.3.2 Creation of Assay Layout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-20
2.4 Scheduling Break . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-24
2.5 Definition of Assay Steps before Read . . . . . . . . . . . . . . . . . . . 2-26
2.5.1 Pipetting Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-28
2.5.2 Wash Steps. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-38
2.5.3 Incubation Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-44
2.5.4 Dispense Steps. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-46
2.5.5 Verify Dispense Steps. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-50
2.5.6 Background Read Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-53
2.5.7 Conditional Delay Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-54
2.5.8 Shake Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-56
2.5.9 Incubate Verification Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-57
2.5.10Clean Washer Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-58
2.5.11 Reagent Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-59
2.6 Read Definition. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-63
2.6.1 Reader Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-64
2.6.2 Background Subtraction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-70
2.6.3 Report Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-73
2.7 Evaluation Definition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-86
2.7.1 Validation Criteria (V. C.). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-87
2.7.2 Qualitative Evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-89
2.7.3 Quantitative Evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-93
2.7.4 Spreadsheet Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-106
2.8 Entry of Logical Functions and Mathematical Signs . . . . . . . 2-108

Gemini - Assay programming manual - Rev. 6 TOC-1

 3 IFA Assay Programming (optional) . . . . . . . . . . . . . . . . . . 3-1
3.1 Introduction and Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
3.1.1 Defining a New IFA Assay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
3.1.2 Defining Assay Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
3.1.3 Editing Existing Assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
3.1.4 Basic Structure of Assay Files . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5
3.1.5 Password Protection for Assays . . . . . . . . . . . . . . . . . . . . . . . . . 3-5
3.2 Assay Protocol Header Information . . . . . . . . . . . . . . . . . . . . . . . 3-6
3.2.1 Creating Slide Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-8
3.3 Assay Layout Definition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-12
3.4 Scheduling Break . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-13
3.5 Definition of Assay Steps. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-15
3.5.1 Pipetting Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-16
3.5.2 IFA Wash Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-17
3.5.3 Incubation Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-19
3.5.4 Dispense Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-19
3.5.5 IFA Dispense Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-19
3.6 Report Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-20
4 Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1

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 Introduction
Typographical Conventions

1 Introduction

Target of this manual is the explanation of the Gemini and Gemini COMBO
instrument, respectively. After having read the manual, the user should be able to
safely operate the Gemini/Gemini COMBO instrument.

1.1 Typographical Conventions

The warnings, notes and symbols described hereafter are used in the current
manual, on the instrument and on its packaging.

1.1.1 Display of Warnings and Notes

DANGER
Danger indicates a hazardous situation that, if not avoided will result in death or
serious injury.

WARNING
Warning indicates a hazardous situation that, if not avoided, could result in death or
serious injury.

CAUTION
Caution indicates a hazardous situation that, if not avoided, could result in minor or
moderate injury.

NOTICE
Notice indicates information considered important, but not hazard-related (e.g.
messages related to property damage). The non-observance of a safety instruction
can result in damage of the instrument or an adverse effect on the instrument
function.

INFO
The non-observance of information can result in an adverse effect on the instrument
function (result deterioration).

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Introduction
Typographical Conventions

1.1.2 Used Warning Symbols

Caution, risk of danger to person or damage to equipment!

Consult instructions for use!

Biohazard!

Electrical hazard!

Laser hazard!

Caution, hot surface!

Mechanical hazard!

Cut injury hazard!

Automatic start-up!

Disconnect mains power connector before servicing!

Consult instructions for use!

Information about the required access rights for Gemini instrument

software functions.

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 Introduction
Typographical Conventions

1.1.3 Special Types

LEDs and LEDs (light emitting diode) and signal lamps are printed in special type.
Signal Lamps Example: Power LED

Fields Fields are printed in bold type.

Example: I D field

Menu items and Menu items and buttons are printed in spaced type.
Buttons Example: Open button.

Keys Keys are printed in slanted type.

Example: Press Enter

File examples File examples are printed in typewriter font.

Example: DRIVER=C:\SERVICE\DRIVERS

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Introduction
Safety Instructions

1.2 Safety Instructions

The following safety instructions shall be observed at all times, both before and
during operation and during maintenance.

Handling of Instructions for use manual

The instructions for use manual is provided for your safety and gives important
instructions for the handling of the instrument described.
• Read all instructions!
• Keep the instructions for use manual nearby the instrument.
• The instructions for use manual shall be accessible to the user at any time.

The Gemini instrument is designed and manufactured in accordance with the safety
requirements for electronic and medical systems. If the law issues regulations
concerning the installation and/or operation of the instrument, then it is the operator's
responsibility to adhere to them.
The manufacturer has done everything possible to guarantee that the equipment
functions safely, both electrically and mechanically. The instruments are tested by the
manufacturer and supplied in a condition that allows safe and reliable operation.

1.2.1 General Safety

Non-observance of safety instructions

The non-observance of safety instructions may result in serious personal injury and
material damage.
• Follow all safety instructions included in this manual.
• Follow all warnings marked on the instrument.

Improper use of the instrument

Improper use of the instrument can cause personal injury, produce erroneous results
and produce damage to the instrument.
• The handling and maintenance of the instrument shall be performed only by
trained and authorized personnel.
• Before operating the instrument, the instruction for use manual shall be
completely read and understood.
• Only use the instrument in accordance with the intended use as described in
this manual.
• Use only the approved consumables and accessories described herein (e. g.
disposable tips, microplates etc.).
• The manufacturer assumes no liability for any damage, including those to
third parties, caused by improper use or handling of the instrument.

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 Introduction
Safety Instructions

Moving barcode scanner

The movement of the moveable barcode scanner can trap you or knock over objects
put down on the loading bay.
• Never enter the loading bay when the instrument is switched on and you
have not received an approval by the instrument!
• Never enter the loading bay before the moveable barcode scanner has come
to a standstill!
• Never use the loading bay as storage space!

Interference by mobile phones

Mobile phones can affect the correct function of the instrument.
• Do not use mobile phones next to a running instrument.

Laboratory equipment
The instrument has been designed and developed as laboratory equipment in
accordance to the requirements of the EC directive 98/79/EC (IVD directive, directive
98/79/EC of the European Parliament and of the Council of 27 October 1998 on in
vitro diagnostic medical devices). In order to assure compliance, applicable
standards recorded in the list of standards harmonized for the IVD directive were
observed. The application of this product for in vitro diagnostics purposes requires a
separate conformity assessment according to EC directive 98/79/EC for the
complete system into which it will be incorporated and/or has to be used in
combination with (e.g. reagent).

Unauthorized changes to the instrument

Any changes to the instrument that are not authorized by the manufacturer will lead
to the loss of the validity of the conformity to the applicable regulations the
manufacturer has declared. In this case, the customer is responsible for the
fulfillment of the applicable regulations.
• Do not perform unauthorized changes.

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Introduction
Safety Instructions

1.2.2 Electrical Safety

Non-observance of rules and regulations

Non-observance of rules and regulations will cause serious personal injury with
deadly consequences and material damage.
• National rules and legal regulations for the safe electrical operation of the
instrument shall be observed.

Improper connection of mains supply

Improper connection of the instrument and the peripheral devices to the mains
supply can cause serious personal injury with potentially deadly consequences and
material damage (e.g. fire).
• Only use grounded connection and extension cables with sufficient capacity
(voltage and current) to connect the instrument and any peripheral devices to
the mains power supply.
• Never remove ground connections.
• Grounding of the instrument and its peripheral devices to the same protective
earth potential shall be ensured.
• The use of a multi-outlet power strip is not allowed!
• Only use power cables that fulfill the minimum requirements for this
instrument.

Damaged power cables

Damaged power cables will cause serious personal injury with potentially deadly
consequences and material damage (e.g. fire).
• Damaged power cables shall be replaced immediately!
• No objects may be placed on the power cables.
• Power cables shall be laid so that they cannot be squeezed or damaged.
• Power cables shall be laid so that they do not lay in accessible or drivable
areas.

Defective instrument
Any defective instrument will result in serious injuries with deadly consequences and
material damage (e.g. fire).
• Immediately disconnect the defective instrument from the mains supply, if a
safe usage is no longer possible.
• Secure the defective instrument against reconnection.
• Label the defective instrument clearly as being defective.

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 Introduction
Safety Instructions

Electric shock by electrical devices on wet surfaces

Working with electrical devices on wet surfaces (floors, work table) will cause serious
injuries with deadly consequences and material damage due to electric shock.
• Only work on dry surfaces (floors, work table).
• Never use the mains supply near liquids and in rooms with high humid.

Replacement of power supply

The power supply contains no serviceable parts! Repairs will cause accidents with
serious injuries with deadly consequences, fire or serious instrument damage.
• Replace the whole power supply when it is faulty!

Emergency shutdown in case of functional disorder

Functional disorder of the instrument will cause electrical shock, burns, cuts or
bruises.
• Use the mains switch to switch off the instrument or the mains plug to
separate the instrument from the mains supply!

Blockade of access to mains supply

Improper placing of the instrument can cause accidents with serious injuries with
deadly consequences, fire or serious instrument damage because the instrument
cannot be switched off or be separated from the mains supply.
• Ensure that the power supply and mains switch are easily accessible.

1.2.3 Laser Safety

Eye injuries due to laser radiation

Laser radiation cause eye injuries when you look into the laser beam.
• Never look directly into the laser beam!
• Do not use optical devices (e.g. mirror).
• Take off watches and mirroring jewelry before operating the laser.
• Be careful during operation and testing the laser of the barcode scanner. A
class 2 laser is used.
• Note that the wrong usage of operating elements or of adjustments or the
non-observance of processes can cause a dangerous emission of laser
radiation.

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Introduction
Safety Instructions

1.2.4 Mechanical Safety

Missing, improperly opened, damaged or opened protective covers

To avoid serious injuries with deadly consequences due to electric shock or injuries
by the instrument (e.g. contusion, cuts etc.), protective covers may only be opened
or removed for certain maintenance procedures and with the highest level of caution.
• Only perform maintenance procedures described in this manual.
• Make sure that nobody is working on the instrument and that all covers are
attached and closed before reconnecting the instrument to the mains supply.
• Make sure that all covers are attached and intact before switching on the
instrument.
• Switch off the instrument, separate it from the mains supply and protect the
instrument against restarting, if protective covers/gears are missing or
damaged.
• Make sure that the motion of the barcode scanner has stopped before
opening covers and/or accessing the working area of the instrument.
• Avoid touching the barcode scanner and other moving parts while the
instrument is in operation.
• Perform all maintenance procedures with the highest level of caution.

Overheating
Improper placing of the instrument may cause fire or serious instrument damage in
case of overheating.
• Do not block or cover ventilation slots.
• The air shall be able to circulate.

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 Introduction
Safety Instructions

1.2.5 Biological Safety

Risk of infection!
The instrument shall be treated as potentially infectious. Improper handling of
infectious parts will cause skin irritations, illnesses and possible death.
• Strictly follow the local and national provisions, legislation and laboratory
regulations.
• Use appropriate gloves!
• Use an appropriate lab coat!
• Use an appropriate eye protection (e.g. protective glasses)!
• Avoid contact between skin/mucous membrane and samples/test reagents or
parts of the instrument.
• Clean, disinfect and decontaminate the instrument immediately if potentially
infectious material has been spilled.
• Do not use broken or chipped tubes or bottles.
• Observe the instructions in the package inserts for correct use of reagents.
• Observe the legal regulations for the handling of infectious material.
• Never use bio-hazardous liquids for testing the instrument!
• The instrument shall be cleaned, disinfected and decontaminated before
servicing!

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Introduction
Safety Instructions

Intentionally left blank.

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 Assay Programming
Introduction and Overview

2 Assay Programming

2.1 Introduction and Overview

The Gemini system is an open system. It allows users to process pre-defined assays
but also to edit existing assays or to create their own assays.

Wrong Results
New, modified or assumed assays must be validated to avoid wrong results.

Defining assays with the Gemini instrument software is facilitated by visual dialog
boxes (no actual programming is needed) but because the instrument is very flexible
and because it allows users to define not only the processing steps but also the result
evaluation steps, defining assays remains a process that must be done with
adequate care and reference to the procedures described in this manual.
This introduction covers the basic concepts of assay files (layout, structure,
protection). The second part is a step-by-step description of how to create completely
new assays.

For assay programming, the use of an external mouse is recommended.

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Assay Programming
Introduction and Overview

2.1.1 Defining a New Assay

In the Gemini program you define a new assay by creating an assay file in which all
assay parameters are entered and saved. All assay files (*.asy) have the same basic
structure, consisting of some defaulted assay steps and a list of freely selectable
assay steps which the user can arrange and define according to his requirements.

Creating a new Proceed as follows:

Assay File 1. Select the F i l e > N e w menu item.
2. Click on the A s s a y symbol.
3. In the S e l e c t A s s a y P r o t o c o l T y p e dialog, the items
C o l o r i m e t e r - E n d p o i n t and C o l o r i m e t e r - K i n e t i c (in
preparation) are displayed.
4. If you will use the multi-preparation function for samples, activate the
checkbox U s e m u l t i - p r e p a ra t i o n s a m p l e s (see chapter 2.1.1.1 on
page 2-5).
5. If you select the item C o l o r i m e t e r - E n d p o i n t, the following window is
displayed:

Figure 2-1: New assay window

1 Assay tree
2 Separating bar (can be shifted)
3 Display area

The display area shows the plate layout with 96 wells and above some default
settings. The assay explorer tree in the left-hand side of this window shows the
basic steps of an assay. You can work with it in the same manner as you work with

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 Assay Programming
Introduction and Overview

the Windows Explorer: a folder including further information is identified by a plus

sign (+). Click on the plus sign to open the folder. An open folder is represented by
a minus sign (- ). Click on the minus sign to close the folder.
The assay explorer tree, henceforth referred to as assay tree, includes the 4 basic
steps of an assay which cannot be deleted:

Assay Header Assay protocol header.

Assay Layout Plate layout definition: layout of samples, standards and
controls on the plate.
Read Execution of reading and evaluation of results
(qualitative or quantitative analysis).
E n d o f Pr o t o c o l End of assay protocols.

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Assay Programming
Introduction and Overview

Show Assay Click with the left mouse button on an assay folder to view the respective assay step
Step with the description of the already defined functions in the display area.

Edit Assay Step To edit an assay step, you always have to select the assay step to be edited.

Insert Assay To insert a new assay step, you always have to select the assay step in front of which
Step the new step is to be inserted.

Context Menu The context menu for inserting new assay steps in a new assay can be selected via
for Inserting the menu item Edit on the menu bar, as well as by clicking the right mouse button on
Assay Steps the step before which the new step is to be inserted.

Figure 2-2: Context menu for inserting assay steps

Undo Revokes the last action you have executed in the assay
tree.
Redo Revokes the last U n d o action again.
Cut Cuts out a highlighted assay step and saves it to the
clipboard.
Copy Copies a highlighted assay step to the clipboard.
Paste Inserts an assay step on the clipboard in front of the
highlighted assay step. Keep in mind, however, that the
given assay structure must not be changed: pipetting
steps must always be inserted before Reading,
evaluations steps always after Reading!
Edit To edit an assay step, you always have to select the
assay step to be edited.
Insert Step To insert a new assay step, you always have to select
the assay in front of which the new step is to be inserted.
Delete Deletes a step highlighted in the assay tree.
Select All Selects all assay steps.
Move Up Moves a highlighted assay step up one step.
Move Down Moves a highlighted assay down one step.
Execute Current Execute only the highlighted step of the selected assay
Step... (see notes below).

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 Assay Programming
Introduction and Overview

Execute Executes all remaining steps included the highlighted

Remaining step of the selected assay (see notes below).
Steps...

Check Results
When you are performing the execute functions it is necessary to check the results
carefully!

When you are performing the execute functions during a running worklist, the plate
will be scheduled into this running worklist!

General buttons
which apply on
OK Saves all entries and returns to the main menu.
most dialog
boxes Apply Saves the entries and the dialog box remains displayed.
Canc el Returns to the main menu without saving any entries.
Data that have already been saved by pushing Ap p l y
remain stored.
Help Calls on-line help.

2.1.1.1 Multi-preparation Assays

A multi-preparation assay supports the usage of different preparations of probes from
a unique sample to transfer them to a single result.

If you use the multi-preparation function, it is not possible to use replicates!

If you have activated the checkbox U s e m u l t i - p r e p a r a t i o n s a m p l e s , then

you have to add the different preparations:

Figure 2-3: Select assay protocol type with multi-preparation function

1. Enter the first preparation name in the input field and click on the A d d
button.
The entered name is shown in the list on the right side. Later, the preparation
names are shown in the plate layout.
2. If wished, choose a color for the preparation in the color list below the names
list. The colors are used in the L o a d dialog.

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Assay Programming
Introduction and Overview

3. Repeat the steps for all preparations.

4. Use the R e m o v e button to delete the selected name.

Later the user must load the preparation sample tubes in the same order as the
preparation names have been entered! All preparation sample tubes are assigned to
the sample ID of the first preparation sample tube!

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 Assay Programming
Introduction and Overview

2.1.2 Defining Assay Steps

Figure 2-4: Assay tree - basic setting

4 Preliminary file name. After saving there is shown the file name of
the assay.
5 Assay steps

Assay Header Double-click on this step to open the respective parameter window (see chapter 2.2 on
page 2-12).

Assay Layout Double-click on this step to open the respective parameter window (see chapter 2.3 on
page 2-18).

Definition of Click with the right mouse button on R e a d to open the I n s e r t S t e p dialog box
possible Assay showing the available steps (see chapter 2.5 on page 2-26).
Process Steps

Figure 2-5: Assay tree with open Read folder - basic setting

Reader Settings Double-click on this step to open the respective parameter window and you can
define the photometer settings (wavelength, etc.) (see chapter 2.6.1 on page 2-64).

Background Double-click on this step to open the respective parameter window (see chapter 2.6.2
Subtraction on page 2-70).

Report Settings Double-click on this step to open the respective parameter window (see chapter 2.6.3
on page 2-73).

Definition of Click with the right mouse button on R e p o r t S e t t i n g s to open the I n s e r t

Evaluation St ep dialog box showing the available steps (see chapter 2.7 on page 2-86).
Steps

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Assay Programming
Introduction and Overview

Saving the As soon as you have defined all steps, select the item F i l e > S a v e A s and save
Assay File the assay under a new name (extension *.asy).

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 Assay Programming
Introduction and Overview

2.1.3 Editing Existing Assays

Proceed as follows:
1. Click on the Op e n button or select the F i l e > O p e n menu item.
2. Click on the Assay Pr otocol F i l e s ( *a s y ) symbol.
3. Select the desired assay file and open it.
4. If necessary, enter the password and confirm with O K .

If you do not know the password, click on the D o n ’ t K n o w P a s s w o r d button.

The assay file will be opened, but you could not edit them.

5. Open folders by clicking on the plus sign (+ ).

6. Assay steps:
• Editing an assay step:
Double-click on a folder whose parameters you want to edit to open the
respective entry window. Enter and save parameters.
• Inserting a new assay step:
With the right mouse button, click on the step in front of which you want
to place the new step or select the menu item I n s e r t S t e p from the
E d i t menu. In the I n s e r t S t e p dialog box, select the desired step
and enter the parameters. Save entries.
• Deleting an assay step:
With the right mouse button, click on the step you want to delete.
Select De le te from the context menu.
7. Save:
• Select the F i l e > S a v e menu item to save the assay under the
same name.
• Select the F i l e > S a v e a s menu item to save the assay under a
new name.

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Assay Programming
Introduction and Overview

2.1.4 Basic Structure of Assay Files

All assay files (*.asy) have the same basic structure, consisting of some defaulted
assay steps (marked with a * in the table below) and a list of freely selectable assay
steps which can be arranged and defined according to the requirements of each test.

Assay Header *
The assay header includes general information such as: assay name, comments (if any),
password protection, written by, creation date, last edited, plate type used, maximum ambient
temperature.
Assay Layout *
Table representation of a test plate showing the respective positions of the samples, standards
and controls for that assay.
Assay steps before Read (Processing steps)
Pipette Inserts a pipetting step (for samples, controls and
standards).
Wash Inserts a washing step.
Incubate Inserts an incubation step.
Dispense Inserts a dispense step (for reagents).
Verify dispense Inserts the verify dispense step (colorimetric verification
for colored reagents).
Background read Inserts a background reading. The baseline is stored and
later subtracted from the measured plate.
Conditional delay Inserts an incubation time; the length can be set relative to
an event on the plate.
Shake Shake on the plate transport unit.
Incubate Verification Incubator performance verification.
Clean Washer Washer manifold maintenance.
Read/Evaluation Settings
Reader settings * Definition of the colorimeter settings.
Background subtraction * Definition of the background calculation method.
Validation criteria Definition of validation criteria.
Qualitative settings Qualitative evaluation.
Quantitative settings Quantitative evaluation.
Spreadsheet Spreadsheet for user-defined calculation operations.
Report Settings *
Definition of the contents of the result printout, of the combined report and of the format and
contents of the result export file.
End of Protocol *

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 Assay Programming
Introduction and Overview

2.1.5 Password Protection for Assays

The A s s a y P r o t o c o l H e a d e r dialog (see chapter 2.2 on page 2-12) includes a
Password field which allows the person who programs the assay to protect it against
editing.
The assay password is completely independent from the general Gemini password
and user rights system. If an assay is protected, it cannot be edited even by users
who are generally authorized to E d i t a s s a y s (see "Instructions for use Manual").
The assay password protection is strictly against editing, i.e. changing any of the
assay steps or parameters defined by the person who wrote the assay.
The password is not required to use the protected assay in a test run. It is not
required either if you just want to open and print the assay (click on the Do n ' t
k n o w p a s s wo r d button in the E n t e r P a s s w o r d dialog.
A password protected assay may be copied and renamed but the copy will also be
protected against editing.

For users who create their own assays, it is strongly recommended that they use the
assay password protection (once they have finished defining an assay). This will
ensure that no accidental change can be made by operators who use the assays for
test runs.

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Assay Programming
Assay Protocol Header Information

2.2 Assay Protocol Header Information

Double-click on A s s a y H e a d e r in the assay tree to open the As sa y

P r o t o c o l H e a d e r dialog.

Figure 2-6: A s s a y P r o t o c o l H e a d e r dialog

Description Name of assay.

Written by Name of the person/company who created the assay
protocol.
Combination Assays belonging to the same combination group can
group be combined on the same plate (provided the assay
parameters are compatible). Assays belonging to
different combination groups cannot be combined on the
same plate (even if they have compatible parameters).
The default combination group for all assays is "0". To
assign an assay to a new group, enter a group number.
Note: The Gemini software does not check compatibility
of shake steps. If an assay that does not need shaking
is combined with a second assay that needs shaking,
the plate will shaken.
For more information on combination groups see
"Instructions for use Manual".
Comments Option to enter additional explanations.
Plat e t ype Select a plate type.
Plat e T y pes Click this button to select the plate type you want to use
for this assay. Moreover, you can load the plate type
editor and create new plate types (see below).

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 Assay Programming
Assay Protocol Header Information

Maximum Enter the maximum permissible room temperature. If

ambient temp. this temperature is exceeded, this will be indicated in the
result file.
Plate ID check Use this field to validate the plate ID.
The field can contain alphanumeric text and/or the
wildcard characters "*" or "?". A "*" is, therefore, always
OK. If the plate ID must start with an A then you would
use "A*". If the plate ID must have an A in the second
position then you would use "?A*".
Example: RUB*
• Plates ID ok:
• RUB20081105-1
• RUBAX_15
• Plate ID not ok:
• TOX20081102-2
• RUG20081105-1
Example: RUB_200?-*
• Plates ID ok:
• RUB_2008-1105-1
• RUB_2007-5
• Plate ID not ok:
• RUB_20081105-1
• RUB_200-5

Note: The minimum entry is a wildcard "*", otherwise

you get an error message.
Pressure Barometric control on aspirate steps.
Monitoring
Define Barcode Enables the dynamic barcode function for the assay
(see Ba rc od e button).
Barcode Allows to define a dynamic barcode format (see
chapter 2.2.2 on page 2-16).
Portfolio group The processing of assays can be limited with assay
portfolio groups. Only assays of the same assay
portfolio group could be used after the entry of an assay
portfolio group name (see also "Instructions for use
Manual", chapter "System Set-up").
Not allowed entries: space characters
Variables Shows the variables used in the assay which can be
deleted by clicking on the D e l e t e button.
If they are used for the assay, they must not be
deleted.
Labels Shows the labels used in the assay which can be
deleted by clicking on the D e l e t e button. Input of the
label or variable is not possible here, but is automatically
carried out by the instrument after they have been
defined in later process steps (see chapter 2.5.1 on
page 2-28 and see chapter 2.7 on page 2-86)
If they are used for the assay, they must not be
deleted.

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Assay Programming
Assay Protocol Header Information

Password Option to enter a password. This rules out that the assay cannot be modified by
anyone who does not know the password. However, no password is required to run
the assay.

Password Enter the password

Retype Repeat the same password.
password

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Assay Protocol Header Information

2.2.1 Creating Plate Types

Click on the Plate Ty pe button to open the Pl a t e T y p e E d i t o r dialog,
showing the plate types available on the instrument and allowing you to generate
new ones. The coordinates of the plate type will be saved to a *.mpc file in the
program directory. The P l a t e T y p e E d i t o r dialog allows you to create new
plate types from existing (*.mpc) files available on the instrument. It does not allow
you to create new (*.mpc) files. If you need to create new (*.mpc) files, please contact
your service engineer.

Figure 2-7: P l a t e T y p e E d i t o r dialog

List of plate types Selection box listing the plate types pre-defined for the
instrument.
Name The name of plate type highlighted in the menu is
displayed. Click on Add to define a new plate type and
enter a new name. This will create a new plate type
which has to be combined with a *.mpc file, i.e. you have
to choose a *.mpc file in the C o o r d i n a t e s drop-
down menu.
Coordinates Drop-down menu showing the available *.mpc files.
These files contain the plate coordinates and are
created using the teacher software.
Rows / C o l u m n s Select the number of rows and columns of the plate
type.
X Offset Possibility to change pipette position from centre of well.
X offset of 0 is recommended.
Add Click this button to create a new plate type. The
previous entry in the N a m e box is deleted. The next
running number is entered as default name, which can
be overwritten. The generated plate type is entered in
the menu to the left and it has to be combined with an
*.mpc file.
Delete Deletes the plate type highlighted in the selection box.
Close Closes the P l a t e T y p e Ed i t o r dialog. Changes
are saved. The program returns to the A s s ay
P r o t o c o l H e a d e r dialog.

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Assay Programming
Assay Protocol Header Information

2.2.1.1 Adding new Plate Types

Proceed as follows:
1. Click on A d d.
The previous entry in the Na me box is deleted and the next running number
is entered as default name.
2. Enter the desired name.
3. In the C o o r d i n a t e s menu, select a suitable microtiter plate parameter
file.
4. Specify the number of R o w s and Co lu mns .
5. Click on A d d to create another plate type.
The previously defined plate type is displayed in the list of available plate
types.
6. Click on C l o s e to accept the generated plate type and to return to the
A s s a y P r o t o c o l He a d e r dialog.

2.2.2 Dynamic Barcodes

This function allows to define a dynamic barcode format for an assay. The dynamic
barcode will be used in the L o t S p e c i f i c V a l u e dialog.

Figure 2-8: B a r c o d e dialog

Available Fields Shows all available fields.

Note: The field A s s a y represents the assay name and
is required.
Available Shows all available containers. Containers are only
Containers used to visualize the corresponding fields. In the
barcode itself, the containers will not be present.
Note: A container must always contains its
corresponding name field.
Separator Field to enter the separator character between the
barcode fields.
Note: The separator is required.

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 Assay Programming
Assay Protocol Header Information

> Adds the selected entry in the A v a i l a b l e F i e l d s list

or the Av a i l a b l e Co n t a i n e r s to the end of:
• the S e l e c t e d F i e l d s list, or
• the selected container in the S e l e c t e d F i e ld s
list.
It isn’t possible to use all available fields or containers in
all situations.
< Removes the selected entry (single entry or complete
container) in the Se l e c t e d F i e l d s list
Selected Fields Shows all entries of the dynamic barcode.
Move Up Moves the selected entry in the S e l e c t e d F i e l d s
list one entry up.
Move Down Moves the selected entry in the S e l e c t e d F i e l d s
list one entry down.
Copy Copies the selected entry in the S e l e c t e d F i e l d s
list and adds it to the end of the list or the container list.
Export Allows to export the defined dynamic barcode.
Import Allows the import of a saved dynamic barcode.
OK Closes the Ba rc od e dialog. Changes are saved. The
program returns to the A s s a y P r o t o c o l H e a d e r
dialog.
Canc el Closes the B a r c o d e dialog. Changes are not saved.
The program returns to the A s s ay P r o t oc o l
H e a d e r dialog.

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Assay Programming
Assay Layout Definition

2.3 Assay Layout Definition

Double-click on A s s ay L ay ou t in the assay tree to open the A s s a y L a y o u t

dialog box.

2.3.1 Assay Layout Dialog Function Overview

Figure 2-9: A s s ay l a y o u t dialog

1 Assay layout for the test plate

2 Label menu. Shows the existing label types for pre-selection. Pre-
select (delete) to clear a well.

Label Displays the name of the label type pre-selected in the

label list (2). This name can be edited here.
Labelling Type of numbering (letters or digital order) to be used for
the selected label.
Colour To better distinguish different labels, you can assign
colors to these labels (default color: black).
Replicates Specify the number of replicates for the highlighted label
(see note below).
Orientation Orientation of replicates:
• C o l u m n s = column-wise;
• R o w = row-wise;
• R a n d o m = random distribution
Fill Orientation General orientation of the orientation of the labels:
• Columns = column-wise
• Row = row-wise

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 Assay Programming
Assay Layout Definition

Randomise The selected labels are randomly distributed over the

plate.
Renumber Updates the consecutive numbering. This may be
necessary, for example, if you have deleted a sample
within a consecutively numbered range, creating a gap.
Fill Fills all blank wells of the plate with the selected label.
Clear Deletes all labels from the plate wells (in the plate
layout).
Undo Revokes the last action. This command can be repeated
several times, so that up to 10 steps can be undone.
Redo Revokes an Undo command again. Can also be
repeated several times (max. 10 times).

If you use the multi-preparation function, it is not possible to use replicates! See also
Multi-preparation Assays (see chapter 2.1.1.1 on page 2-5).

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Assay Programming
Assay Layout Definition

2.3.2 Creation of Assay Layout

A plate layout with 96 fields corresponding to the layout of a microtiter plate is
displayed (see chapter 2.3.1 on page 2-18), numbered consecutively (default setting T1
to T96, with T = test (sample)).
Here you define how to distribute the controls, standards and samples on the test
plate, by providing the individual wells with a coded Label. Either clear all previous
labels with <Clear> or individual field labels by selecting the function (delete) in the
menu and then select the label you want to remove.

2.3.2.1 Label Menu

The letters in that menu correspond to the individual well types. The well type
highlighted in the menu is active and is entered into the sample matrix with the mouse
pointer, by highlighting a blank well or several blank wells.
If (delet e) is pre-selected, the content of all selected wells is cleared.

B Blank well (Blank)

This blank reader value can be subtracted from the reader values of other
well types.
S Standard (Standard).
Standards are used in the Q u a n t i t a t i v e S e t t i n g s for generation of
standard curves.
T Test (sample).
Test are used as samples.
NC Negative control
PC Positive control
C O Cutoff

You may define further labels (see below).

The label type highlighted in the Label list is active. If you select a label type in the
Label list and click on an empty well in the Plate Layout, the respective label is
entered. If you select several empty wells in the Plate Layout, the respective label is
entered in all selected wells with consecutive numbering (see below).
If (delete) is pre-selected, the contents of all selected wells is cleared.

Only standards can be taken into account in the quantitative analysis. But in some kit
inserts, standard O is deemed to be a "negative control". In this case, users should
redefine this "control" as a standard in order to maximize the number of data used to
build the signal/concentration curve.

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 Assay Programming
Assay Layout Definition

2.3.2.2 Consecutive numbering

If several samples of the same type have been selected, the samples are numbered
as follows:
• If you select a well area, this area is numbered consecutively column-wise or
row-wise, depending on the setting in the F i l l O r i e n t a t i o n box.
• If you select another well area for the same well type, the consecutive
numbering is continued accordingly.
• Selected single wells are numbered in the order of their selection (i.e. not
column- or row-wise).
• If several replicates have been pre-selected, each number of the consecutive
numbering is automatically repeated corresponding to the number of
replicates.

2.3.2.3 Information on the selected Well Type

For each highlighted well type, the following information has to be entered before
you fill in the plate layout:
1. Edit label in the L a b e l box.
The label selected in the label menu is displayed in the L a b e l box and can
be edited there. Any changes are immediately transferred to the label menu.
If you want to add a new label, duplicate the label highlighted in the selection
box by clicking on Add and then change it in the L a b e l box.
2. Select numbering type in the L a b e l l i n g selection box.
The type of numbering used (digit or letter) is displayed in the L a b e l l i n g
box and can be selected there.
3. Select label color in the C o l o u r selection box
You can select the color for the active label on the screen to distinguish the
different well types.
4. Define number of replicates in the R e p l i c a t e s edit box.
Enter the number of replicates for the well type highlighted in the menu.
Depending on this definition, each number is repeated automatically, when
the labels of this well type have been entered in the matrix.

2.3.2.4 Select Orientation of numbering for Replicates in the

Orientation Selection Box
Proceed as follows:
1. Select the direction of label numbering for replicates: column- or row-wise or
random.
2. Select general numbering direction in the F i l l O r i e n t a t i o n selection box:
column-wise, row-wise or random.

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Assay Programming
Assay Layout Definition

2.3.2.5 Filling the Plate Layout

A well has to be empty before you can fill it. The actions described below do not allow
you to directly "replace" one label type by another. If the wells you want to fill are not
empty, you first need to clear them (as described on the previous page).

Individual wells:
1. Select well type in the menu and define the respective parameters.
2. Click consecutively on the wells to be filled with this well type. The label is
entered with consecutive numbering.

Well ranges:
1. Select well type in the menu and define the respective parameters.
2. With the mouse pointer, highlight the desired area: Highlight a row from left to
right or a column from top to bottom or a rectangular range from the top left
corner to the bottom right corner. The well type is entered in the highlighted
range with a consecutive number.

Figure 2-10: Selecting the well range

Filling all blank wells:

1. Select well type in the menu and define the respective parameters.
2. Click F i ll . All blank plate positions are filled with the selected label and the
selected number of replicates.

If you use the multi-preparation function, then you must select at least as many wells
as you have different preparations (see chapter 2.1.1.1 on page 2-5).

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 Assay Programming
Assay Layout Definition

2.3.2.6 Add Label to Selection Box

Proceed as follows:
1. First you have to create a new label by duplicating an existing label.
Highlight a label in the selection box and click on A d d. The highlighted label
is duplicated and displayed in the L a b e l box (Label C ).
2. Correct the label as needed in the L a b e l box.

New Label
The new label has not the same functions as the original label!

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Assay Programming
Scheduling Break

2.4 Scheduling Break

Only for instruments with Gemini instrument COMBO software!

All assay steps from all assays of the worklist programmed before the schedule
break will be performed in advance.
The S c h e d u l i n g b r e a k step can be changed by the M o v e u p and M o v e
d o wn functions in the Context Menu for Inserting Assay Steps.
Example:
The assay has at first the pipette step, followed by the schedule break and a
dispense step.

Figure 2-11: Assay with scheduling break

The scheduling shows, that at first the sample pipetting of both plates will be
performed; after this step, the two plates are scheduled according the remaining
assay steps.

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 Assay Programming
Scheduling Break

Figure 2-12: Worklist with scheduling break

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Assay Programming
Definition of Assay Steps before Read

2.5 Definition of Assay Steps before Read

An assay is programmed by adding individual processing steps.

Click with the right mouse button on R e a d in the assay tree (see chapter 2.1.2 on
page 2-7) and then select I n s e r t S t e p in the menu window. The I n s e r t S t e p
dialog box is displayed, showing the assay steps you can select.

Figure 2-13: I n s e r t S t e p dialog

Pipette Inserts a pipetting step to aspirate/dispense samples

and controls (see chapter 2.5.1 on page 2-28).
Wash Inserts a wash step (see chapter 2.5.2 on page 2-38).
Incubate Inserts an incubation step (see chapter 2.5.3 on page 2-
44).
Dispense Inserts a dispense step (see chapter 2.5.4 on page 2-46).
Verify dispense Inserts a verify dispense step to check (photometer) if a
dispense step was correctly carried out (see chapter 2.5.5
on page 2-50).
Background Inserts a background reading step (see chapter 2.5.6 on
read page 2-53).
Conditional Defines a variable incubation time, which depends on e.
delay g. reaching an O.D. value (see chapter 2.5.7 on page 2-54).
Shake Definition of shake parameters on plate transport unit
(see chapter 2.5.8 on page 2-56).
Incubate Used for performance verification purposes only (see
Verification chapter 2.5.9 on page 2-57).
Clean Washer Used for maintenance purposes only performs cleaning
of the washer head for 15 min. (see chapter 2.5.10 on
page 2-58).

After selection of a step the respective dialog box is displayed for parameter entry.
Once you have entered your parameters and saved your entries, the new step is
inserted in the assay tree.

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 Assay Programming
Definition of Assay Steps before Read

Order of Assay You can arrange the individual steps in any order. The order is defined during new
Steps definition of a step by clicking with the right mouse button on the folder before the
one you the want to place the new step.
But when defining your steps, you can freely add them in any order to start with
(some are easier to define than others) and then rearrange them in the correct order
of the assay with the M o v e U p / M o v e D o w n items of the E d i t menu (or of
the context menu).

Editing Assay Double-click on the respective symbol in the assay tree to open the respective
Steps parameter window.

Replicate steps If your assay includes steps that are repeated twice identically or almost identically
(this is often the case for W a s h steps or I n c u b a t i o n steps), you can speed up
the definition process by using the C o p y / P a s t e function of the E d i t menu (or
of the context menu). Edit the parameters if necessary.

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Assay Programming
Definition of Assay Steps before Read

2.5.1 Pipetting Steps

The P i p e t t e dialog lets you define how the samples and controls will be aspirated
from one location and dispensed into another (e.g. for samples, from test tubes to
test plate). When dispensing to a test plate you also define the well(s) to pipette into.

The P i p e t t e dialog is also used to define predilution steps. In this case, it is used
not only to define the aspiration and dispense of samples and controls but also of
reagents (e.g. diluents) into the dilution plates (or tubes).

Select P i p e t t e in the I n s e r t S t e p dialog (or double-click on the Pipette folder

in the assay tree) to open the following dialog:

Figure 2-14: P i p e t t e dialog: definition of pipetting steps

Here you define the wells to pipette into and the pipetting steps to be performed.
Several sub-steps can be performed in one pipetting step (step1, step2...).

Plate layout The plate layout defined in assay layout definition (see
chapter 2.3.2 on page 2-20) is displayed. Default setting is
that all wells have a checkmark. A checkmark in the
Plate Layout means that pipetting is performed into the
respective well. Click on a well to remove the respective
checkmark (= deselect the pipetting function); click
again to add the checkmark again.
S t e p s list Menu displaying the pipetting steps that have been
defined. Default setting if no step has yet been defined
is St ep 1 . You can edit the step name in the E d i t
O p e r a t i o n s dialog.
New Step Adds a new pipetting step to the S t e p s menu (default
is Step1, Step2...).
Delete Step Deletes the highlighted pipetting step in the S t e p s
menu. The button is not available, when only one step
exists because this step cannot be deleted.

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 Assay Programming
Definition of Assay Steps before Read

Edit Opens the E d i t O p e r a t i o n s dialog and you can

Operations... define individual pipetting functions such as aspirate
and dispense (see page 2-31 and following pages).
Eliminate assay This option can be selected for each step defined in the
drift caused by pipette dialog of the assay.
this operation The software will calculate the time required for all
pipette steps where the option El i m i n a t e a s s a y
d r i f t c a u s e d b y t h i s o p e r a t i o n is enabled.
The first cycle of the following wash steps is delayed
according the duration of the previous calculated pipette
time.
Pipette time (Eliminate assay drift enabled) = Time
for first wash cycle
The sequence of the following wash step is:
1. Aspirate / Dispense first strip – first wash cycle
2. Delay (according calculated pipette time)
3. Aspirate / Dispense second strip – first wash cycle
4. Delay (according calculated pipette time)
5. ...
6. Aspirate / Dispense last strip – first wash cycle
7. Aspirate / Dispense remaining wash cycles without
delay
8. Final aspirate cycle

Pipette time = Total time of steps 1 to 6

For more information, see chapter 2.5.1.4 on page 2-36.

See note below!

Action On Error Here you can define how the instrument should respond
to a pipetting error:
• Raise alarm and stop
• Log and continue
Document error and continue, if possible.
• Manually pipette at end of step
The M a n u a l Pi p e t t i n g dialog shows all
relevant data required to perform the missed pipette
sequence manually.
Each pipetting error is documented by the instrument
and is entered in the event log. In the results, affected
wells are flagged.
Layout... Opens the A s s a y L a y o u t dialog, and you can make
corrections, if necessary (see chapter 2.3 on page 2-18).

Incompatible functions
Note that the function E l i m i n a t e a s s a y d r i f t c a u s e d b y t h i s
o p e r a t i o n is strictly incompatible with the worklist option m u l t i p i p e t t i n g (see
"Instructions for use Manual")!

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Proceed as follows:
The plate layout defined in assay layout definition (see chapter 2.3 on page 2-18) is
displayed in this window. Default setting is that all wells have a check mark and step
1 (1st pipetting step) is displayed in the S t e p s menu. A check mark in the plate
layout means that pipetting is performed into the respective well. Click on a well to
remove the respective check mark (= deselect the pipetting function); click again to
add the check mark again.
Now you can define the various pipetting steps in accordance with your assay:
1. Deselect wells for S t e p 1 which should not be pipetted into.
2. Click on E d i t O p e r a t i o n s . . . and define the individual pipette functions
and the respective parameters for S t e p 1 in the Ed i t O p e r a t i o n s
dialog (aspirate, dispense). You can change the name St ep 1 as you wish
(see chapter 2.5.1.1 on page 2-31). The default setting W a s h always has to be
enabled to ensure that the pipette tip is replaced after each pipetting step.
3. Click O K to confirm the entries in the E d i t O p e r a t i o n s dialog. The
program returns to the P i p e t t e dialog.
4. Click on N e w S t e p to define a second pipetting step. In the St ep s
menu, S t e p 2 is displayed and highlighted. In the plate layout, all wells
have a check mark. Define the wells for this step to which the pipetting
functions will apply; then click on E d i t O p e r a t i o n s . . . to define the
individual pipetting functions in the E d i t O p e r a t i o n s dialog.
5. Further steps can be defined.
6. If you highlight a step in the S t e p s menu, the respective plate layout (the
wells with defined pipetting functions and in the E d i t O p e r a t i o n s dialog
the defined pipetting functions) is displayed automatically. You can view the
respective parameters in the respective dialog boxes and edit them, if
necessary.

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 Assay Programming
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2.5.1.1 Edit Operations Dialog

Click on E d i t O p e r a t i o n s . . . to open the E d i t O p e r a t i o n s dialog and
define the pipetting functions for the respective step.

Figure 2-15: E d i t O p e r a t i o n s dialog

Click on one of the buttons to open the respective dialog and enter the respective
parameters. If you confirm the parameters with O K , the step is entered in the
Op e r a t i o n s menu before the highlighted position. The steps W a s h / T i p
eject and < E n d > are always defaulted and must remain in the menu. Double-
click on a row in the menu to edit the values of an already defined step. The
respective parameter window opens.

Description Description of pipetting step. This name can be edited. It

is displayed in the St ep s list in the P i p e t t e dialog.
Operations Lists all operations that are combined in the step
displayed in the D e s c r i p t i o n field.
Defines aspiration of reagents or samples (see
chapter 2.5.1.2 on page 2-32).

Defines the dispensing of reagents or samples (see

chapter 2.5.1.3 on page 2-34). This button is enabled only
when the aspirate function has been defined.
Defines the wash function. No entries are required since
the Gemini instrument is provided with disposable tips.

Edits the steps highlighted in the O p e r a t i o n s menu.

Editing is also possible by double-clicking on the
respective step.
Removes the highlighted steps from the O p e r a t i o n s
menu.

Move Up Moves the highlighted step in the O p e r a t i o n s menu

up one row.
Move down Moves the highlighted step in the O p e r a t i o n s list
down one row.

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2.5.1.2 Aspirate Parameters

Click the aspirate button in the E d i t O p e r a t i o n s dialog to open the A s p i r a t e

dialog.

Figure 2-16: A s p i r a t e dialog

Volume Enter the aspirate volume. To ensure precise pipetting,

the aspirate volume can be set larger than the dispense
volume.
Note: In that case, please make sure that no mix
cycle is later defined!
Volume Offset Select the volume offset for the different dispense
modes to enable the volume offset. The volume offsets
are fixed in the software and can’t be modified or
changed.
F r om Define from where the reagent or sample is to be
aspirated. M i c r o p l a t e refers to the test plate,
S a m p l e s a m p l e refers to the sample tubes in the
sample racks, D i l u t i o n p l a t e refers to a plate
placed in the dilution area, T e s t T u b e refers to
dilution tubes (placed in the sample racks if pre-dilution
is done in tubes), R e a g e n t refers to all available
reagents (including controls and standards).
Note: Microplate refers to a test plate. However,
samples can only be aspirated from sample tubes or
from a dilution plate. Aspiration from a test plate is not
possible.
Label Applies to dilution plates or tubes only. If you use more
than one dilution plate or tube, you have to affect a label
to each plate (or tube) so that the pipettor knows from
which plate (or tube) it should aspirate.
Reagent The R e a g e n t drop-down list is enabled if you have
selected reagents in the F r o m list. You have to specify
the reagent to be aspirated. If the desired reagent is not
yet included in the list, you can enter it by clicking on the
R e a g e n t s . . . button (see chapter 2.5.11.1 on page 2-
59).

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U s e d e f a u l t p r e - Minimum volume as defined in the system setup is

dilution used.
minimum volume
Alternative Minimum volume can be set directly.
minimum volume
Aspirate profile Select the desired aspirate profile. The aspirate profile
you define here will apply to both samples and reagents
(controls, standards or diluents). Note that, for reagents,
it will override the aspirate profile defined in the E d i t
R e a g e n t D e t a i l s dialog (see chapter 2.5.11.2 on
page 2-60).
On pipetting profiles in general, see "Instructions for use
Manual".
Aspirate Check If this item is checked, the instrument verifies if a dive
out position is detected when retracting the tip after the
aspirate operation and if the difference between dive in
and dive out position is in accordance with the
calculated drop of the liquid surface. This function
ensures the pipetting and dramatically reduces the risk
of false pipetting.
Pressure If this item is checked and pressure monitoring is
Monitoring activated in the assay header (see chapter 2.2 on page 2-
12), the air pressure in the pipetting system is monitored
during the aspirate and the data are compared with
standard values for a liquid type. This function ensures
the pipetting and dramatically reduces the risk of false
pipetting.
Liquid Type If pressure monitoring is used, a liquid type has to be
selected to obtain standard values for pressure
measurements.
Reagents Opens the S e l e c t R e a g e n t s dialog (see
chapter 2.5.11.1 on page 2-59), listing the reagents
available in this system. You can select the existing
reagents for the aspirate function. Moreover, you can
enter new reagents.

Wrong results/spillage
It is necessary to validate pipetting profiles with affected assays to avoid wrong
results or spillage.

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2.5.1.3 Dispense Parameters

Wrong results
All assays using multishots must be validated for their respective number!

Incompatible Functions
Do not confuse this Dispense sub-step, which is defined (within the Pipette step) for
samples and controls (or reagents/diluents when they are dispensed into a dilution
plate), with the actual Dispense step which is used for reagents dispensed into test
plates (see chapter 2.5.4 on page 2-46).

Click the dispense button in the E d i t O p e r a t i o n s dialog to open the

D i s p e n s e dialog.

Figure 2-17: D i s p e n s e dialog

Volume Define the dispense volume in µl.

If you specify a dispense volume which is larger than the
aspirate volume, an error message stating "Insufficient
aspirate volume for the required dispenses" is
displayed.
Note that the dispense volume must not be lower than
the specified minimum volume.
Volume Offset Select the volume offset for the different dispense
modes to enable the volume offset. The volume offsets
are fixed in the software and cannot be modified or
changed.

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In liquid If this item is checked, the system starts by dispensing

dispense the Z - m a x v o l u m e at the Z-max position (deepest
position) and dispenses the remaining volume with
reverse tracking of the pipettor. This option is useful as it
prevents splashing and reduces significantly the risk of
contamination when dispensing controls and samples.
Z-max volume Define the volume which is dispensed at the Z-Max
position before the system starts dispensing the
remaining volume with reverse tracking of the pipettor.
Example 1:
• Volume = 100 µl
Z-Max Volume = 50 µl
The pipettor moves to the Z-max position (LLD not
active), dispenses 50 µl and starts dispensing the
remaining volume of 50 µl with reverse tracking.
To be sure that the tip is at liquid interface after the
Z - m a x v o l u m e is dispensed, the Z - m a x
v o l um e should be equal or a little bit higher than
the equivalent volume of the Z - m a x v o l u m e.
Example 2:
• Volume = 100 µl
Z-Max Volume = 0 µl
The pipettor moves to the liquid surface (LLD active)
and starts dispensing the dispense volume of 100 µl
with reverse tracking.
To Select the target for the dispense operation from the
drop-down list. M i c r o p l a t e refers to the test plate,
D i l u t i o n p l a t e refers to a plate placed in the dilution
area, T e s t T u be refers to dilution tubes (placed in
the sample racks if pre-dilution is done in tubes).
Label Applies to dilution plates or tubes only. If you use more
than one dilution plate or tube, you have to assign a
label to each plate (or tube) so that the pipettor knows
into which plate (or tube) it should dispense.
Multishots Several dispensing steps can be performed.
Prerequisite is that a multiple of the dispense volume
has been aspirated using the aspirate function, so that
the contents can be dispensed (e.g. aspirate 300 µl and
dispense 3 x 100 µl).
See note above!
Dispens e pr ofile Select the desired dispense profile. The dispense profile
you define here will apply to both samples and reagents
(controls, standards or diluents). Note that, for reagents,
it will override the aspirate profile defined in the E d i t
R e a g e n t D e t a i l s dialog (see chapter 2.5.11.2 on
page 2-60).
On pipetting profiles in general, see "Instructions for use
Manual".

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Back to sour ce If oversoak volume is defined (i.e. the volume aspirated

is larger than the volume being dispensed), you may
move the excess volume back to the reagent container
or discard it. The volume entered here in µl indicates the
volume that is to be moved back to the reagent
container.
This function is rarely used for samples and controls
because of the potential contamination risk.
No. of mix Number of mix cycles for optimum mixing. A mix cycle
cycles consists of aspiration and dispensing of the liquid within
a well.
Volume to mix Define the volume to be used for mixing.
with The volume is only considered when the N o . o f m i x
c y c l e s is not 0.
Use alternative Enable and select an alternative plate coordinate file
coordinate file (*.mpc) for that step. In this case a different Z dispense
height can be used instead of the default height of the
plate type selected in the A s s a y H e a d e r dialog (see
chapter 2.2 on page 2-12).

Wrong results/spillage
It is necessary to validate pipetting profiles with affected assays to avoid wrong
results or spillage.

Incompatible functions
Do not use the B a c k t o s o u r c e function together with multiaspirate step
(several aspirate steps)!

2.5.1.4 Eliminate Assay Drift

Incompatible functions
Note that this function is strictly incompatible with the worklist option m u l t i
p i p e t t i n g (see "Instructions for use Manual")!

If assays are combined on one plate, where only one assay has the assay drift for
pipette/wash step enabled, the software applies the drift compensation on all assays
on the plate!

Because pipetting samples (or dispensing reagents) into a whole plate can be fairly
long, the time span between the moment when the first strip and the last strip of a
plate is pipetted (dispensed) can be significant. But then, when these strips get
washed, they get washed almost simultaneously (as the washer operates much
faster than the pipettor). In other words, the waiting time between pipetting
(dispensing) and washing is much longer for the wells of the first strip than for those
on the last strip.

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In some assays, this can create problems (inconsistent results from one strip to the
other).
The purpose of the E l i m i n a t e a s s a y d r i f t caused by this operation item
available in the P i p e t t e and in the D i s p e n s e dialog is to correct this.
If you check this item in the P i p e t t e dialog, the system delays the first wash cycle
of each strip in such a way that the time span between pipetting (dispensing) and
washing is the same for each strip (Time needed to pipette all the samples / controls
= Time used to perform the first wash cycle of the following wash step).
If you check this item in the D i s p e n s e dialog, the system monitors the time
needed to dispense the reagent into the whole plate and delays the first wash cycle
accordingly (Time needed to dispense the reagent = Time used to perform the first
wash cycle of the following wash step).
Because the E l i m i n a t e a s s a y d r i f t function results in an increase (for all
strips except the first one) of the waiting time span between pipetting (dispensing)
and washing, the duration of the plates room-temperature incubation between those
two steps has to be reduced accordingly. This reduction would be different for each
strip, and therefore be difficult to define.
Instead, you just need to check the incubation time from the start of the previous
assay step item in the I n c u b a t e dialog (see chapter 2.5.3 on page 2-44). The system
then calculates the incubation time from the start of the pipetting (dispensing) step.
That way, all strips will have an identical incubation time.
This feature works only for room-temperature incubation.
Example:

Figure 2-18: Assay Drift

In case 1, with drift elimination, you can see that each strip gets a precise 30 min.
waiting time (room-temperature incubation) between pipetting and its first wash
cycle. In case 2, without drift elimination, only the last strip gets an adequate waiting
time of 30 min., all the other strips get an extended waiting time.

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2.5.2 Wash Steps

Here you define the parameters used when test plates are washed in the wash unit.
Normally, a wash step includes several wash cycles. The W a s h dialog lets you
define different parameters for the first wash cycles and for the last wash cycle. The
first wash cycles include dispense and aspirate functions, the last wash cycle is
aspirate only.
Select the W as h item in the I ns er t S t e p dialog (see chapter 2.5 on page 2-26).
The W a s h dialog appears.

Figure 2-19: Wash dialog

Wash Buffer To select the wash buffer, click the arrow button to open the drop-down list. If the
desired buffer is not included in the list you may define it by clicking the B u f f e r s
button (see chapter 2.5.11.1 on page 2-59).

Buffers If the desired buffer is not available in the drop-down list,

you may define or load another wash buffer by clicking
this button to open the S e l e c t R e a g e n t s dialog
with the wash buffers available on the system. Select
the desired wash buffer to be used with the respective
assay (see chapter 2.5.11.1 on page 2-59).

Strips Select the strips to be washed. Each box corresponds to a strip. The strips marked
by a check mark are washed. To remove/add a check mark, click on the respective
strip number.
Under default settings, all strips are checked. If, for example, you use plates with
removable strips without including all 12 strips, make sure that you uncheck the
boxes corresponding to the strips not included. On defining different wash
parameters on the same plate or on defining a strip-wise washing mode, see below.

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It is useful to mark all strips. The system does not wash unused strips.

Heights Automatic or freely definable height settings for the washer head. In case the
automatic height dialog is enabled, the heights defined in the S y s t e m S e t u p . . .
/ W a s h e r will be used. In this case, the respective edit box is disabled. To freely
define the height setting, uncheck the box and use the edit box on the right to specify
a value. You can visualize the respective height setting through the window on the
front panel of the instrument.

Top wash height The wash head is on the level of the upper edge of the
well, i.e. higher than during dispensing. 0 = highest
position of dispensing needle.
Bottom wash The wash head is directly above the well bottom =
height height for executing the bottom wash function, i.e.
intense washing of the wells.
Aspirate height Height of the wash head during aspiration.

Wash Mode
List Use the drop-down list to select the wash mode:
• Plate wash mode
In a plate-wise washing mode, the washer performs
the first wash cycle on the whole plate, then the
second wash cycle on the whole plate, etc. until the
complete wash step is finished.
• Strip wash mode
In a strip-wise washing mode, the washer performs
all the wash cycles included in the wash step on the
first strip, then all the wash cycles on the second
strip, etc.

Note: Default setting is P l a t e w a s h m o d e . S t r i p

w a s h m o d e can induce assay drift and/or well
dehydration. It is recommended to select S t r i p w a s h
m o d e only if it is absolutely required for a specific test
and with proper validation (see chapter 2.5.2.1 on page 2-
42)).
R e s e t a s s a y d r i f t This item applies only if S t r i p w a s h m o d e has
been selected in the drop-down list above.

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Purge The washer's Purge and Clean sequences are normally defined at system level (see
"Instructions for use Manual" - "System set-up - Washer tab") and are identical for all
assays. The Purge and Clean fields in this dialog allow you to define assay-specific
Purge and Clean settings, for example for assays using special reagents that require
a more thorough Purge or Clean function or a different clean fluid.

If purge volume and cleaning parameters are changed, the default values are
overridden.

U s e s y s t em Check this item if you want to use the default washer

defaults purge settings as defined in the system set-up (see
"Instructions for use Manual" - "System set-up - Washer tab").
Uncheck this item to define assay-specific V o l u m e
settings.
Volume Enter the volume to use per manifold needle for the
Purge function. The liquid used is the wash buffer
selected in the W as h b u f f e r drop-down list (see
above).

Clean See above under Purge.

U s e s y s t em Check this item if you want to use the default washer

defaults clean settings as defined in the system set-up (see
"Instructions for use Manual" - "System set-up - Washer tab").
Uncheck this item to define assay-specific V o l u m e
and F l ui d settings.
Volume Enter the volume to use per manifold needle for the
Clean function.
F l ui d Select the liquid (wash buffer, clean fluid, etc.) you want
to use for the Clean function.

Dispense Parameters of all the wash cycles before last. These parameters include aspirate
and dispense parameters.

T op w a s h Wash volume per well (normal washing) in µl. During

volume (µl) dispensing a permanent vacuum is applied to the
aspiration needles to rule out any overflow of wash
buffer.
No. of cycles Number of wash cycles per wash step.

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Aspirate mode Specify the aspiration mode depending on the microtiter

plate type used.
• Centre
The needle position when aspirating is in the centre
of the well. This mode is adequate for plates with
round-bottom wells.
• Sweep
When aspirating the needle position moves from one
side of the well to the other. This is recommended for
flat bottom test plates. However, as it makes the
aspiration process last longer, it is recommended
mostly for the final aspiration.
Min. cycle time 1 cycle = 1 plate. Specify the minimum time for one
(secs) cycle. Enter the minimum soak time of the wash buffer.
Dispense rate The dispense rate defines the pressure or the speed,
respectively, with which the wash buffer is dispensed
into the wells in percent of the pumping capacity.
Dispense as If this item is selected, the wash heads dispenses wash
head rises fluid already while moving upward.
Partial plate Defines the speed of processing a partially loaded plate.
mode • As Quick As Possible
In this mode only the defined strips are washed. After
washing the last strip, the system immediately starts
all over again.
• Maintain Full Plate time
In this mode, the wash head moves to each strip, so
that the same dwell-time of the wash buffer is
ensured even for partially loaded plates.
Bottom wash Volume at bottom wash function in µl. Enter the volume
volume (µl) per well for tests requiring bottom wash.
No. of cycles Number of wash cycles including bottom wash (e. g.: "1"
indicates that each normal wash cycle will include a
bottom wash function).

Aspirate Aspiration step after the last wash step to empty the plate.

No. of cycles Number of aspiration cycles.

Aspirate mode Specify the aspiration mode depending on the microtiter
plate type used.
• Centre
The needle position when aspirating is in the centre
of the well. This mode is adequate for plates with
round-bottom wells.
• Sweep
When aspirating the needle position moves from one
side of the well to the other. This is recommended for
flat bottom test plates. However, as it makes the
aspiration process last longer, it is recommended
mostly for the final aspiration.

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Partial plate Defines the speed of processing a partially loaded plate.

mode • As Quick As Possible
As soon as a wash cycle has been performed during
the wash step the next wash cycle is started even if
the plate is washed partially.
• Maintain Full Plate time
Independently of numbers of strips to be washed in
this wash step every strip position of the plate is
moved to the washer head. Only the assigned strips
are washed. This leads to an equivalent soak time
even if the plate is not processed completely.
Final aspirate Here the minimum time consumption for performing the
minimum cycle last aspirate cycle can be entered after checking the
time (secs.) check box. This allows to accept the duration for the last
aspirate step to the duration of a subsequent dispense
step.

2.5.2.1 Strip Wash Mode

Assay Drift If you select S t r i p w a s h m o d e , this means that each strip is washed at a
slightly different time than the others. This "waiting time", for example between the
moments the wash step is completed on the first strip and the moment the wash step
is completed on the last strip is equivalent to a longer room-temperature incubation
(for the first strip). In some assays, this "drift" effect can have adverse consequences
on the results.

Using strip wash mode for long wash cycles can lead to assay drift and/or well
dehydration. For such assays use P l a t e wa s h m o d e or skip final aspiration
during strip wash mode and insert second wash step for final aspiration to avoid wells
fall dry.

If the R e s e t a s s ay d r i f t item is checked, the system compensates this drift

effect by rescheduling the following pipette, dispense or wash steps so that the
"room-temperature incubation time" for each strip is identical.

Well Generally, a wash step includes one or more wash cycles followed by a final
dehydration aspiration of the liquid from the plate wells.
In Pl a t e w a s h m o d e , the final aspiration is performed almost simultaneously
on all strips at the end of the complete wash step.
In S t r i p w a s h m o d e , the complete wash step, including the final aspiration, is
performed individually on each strip. This means that the first strip will be aspirated
a relatively long time before the last strips on the plate (the exact time difference
depending on the duration of the wash step and the number of strips used). The
result of this is a risk of dehydration of the wells of the first strips. To avoid this, you
can, if the assay absolutely requires a S t r i p w a s h m o d e , program two
consecutive wash steps instead of one: the first one in Strip mode without aspiration
and the second one in Plate mode with only the final aspiration.

If you have any doubt about when and how to use the Strip wash mode option,
please call your application engineer for assistance.

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Incompatible functions
Avoid combining assays with Plate wash mode and assays with Strip wash mode
on the same plate! This could result in a delayed final aspiration including on the
Plate wash mode assay.

2.5.2.2 Defining different Wash Parameters on one Plate

You can only define one set of wash parameters for each wash step. The only option
you have is to specify (in the Strips field) that some strips are not washed but you
cannot specify different wash parameters (e.g. different wash buffers) for different
strips on the same plate in the same wash step.
If you want to do so, you have to create several consecutive wash steps and select/
deselect the respective strips (e.g. wash step 1 will use wash buffer X on strips 1 to
6, wash step 2 will use wash buffer Y on strips 7 to 12). The system will then be able
to adjust and apply the different wash parameters to different strips on the same
plate.

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2.5.3 Incubation Steps

Select the I n c u b a t e item in the I n s e r t S t e p dialog (see chapter 2.5 on page 2-
26) to open the I n c u b a t e dialog.

Figure 2-20: I n c u b a t e dialog box

It is possible to perform an incubation step as part of the semi-automatic mode.

Temperature Select the incubation temperature.

Room Room temperature (RT). Because of the heating due to

temperature the instrument itself, it is generally estimated that the
"room-temperature" inside the instrument can be up to
5°C higher than the actual "room temperature" in the
rest of the room.
T em p e r a t u r e Enter the temperature required (room temperature +
5°C up to 50°C) and tolerance and the acceptable
temperature limits (e.g. +/- 1°C).

Duration Define the incubation time in minutes.

Incubate for Select the minutes by clicking on the respective arrow

buttons or inserting the value in the box.
T ol e r a nc e Select the tolerances for the incubation duration (e.g. +/-
2 minutes).
Time incubation This feature applies only to room-temperature
from start to incubation. If this item is checked, the incubation
prev ious ass ay duration you have specified above is timed from the
st ep start of the previous (P i p e t t e or D i s p e n s e) assay
step. You should check this item only if you have
checked the Eliminate as say drif t caused by
this operation item in the P i p e t t e or in the
D i s p e n s e dialog. For more information on this
feature, see chapter 2.5.1.4 on page 2-36.

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Incompatible functions
This function is strictly incompatible with the worklist option m u l t i p i p e t t i n g (see
"Instructions for use Manual")!

Required This function is not used for the Gemini instrument.

Lighting Level
Ambient light Not used.
levels
Dark Not used.
Don't care Default setting.

Shaking Enter the shaking parameters for one incubation step. This applies only to heated
incubators. For plates which need shaking but do not need heated incubation, you
can define an independent S h a k e step (see chapter 2.5.8 on page 2-56) or enable
shaking prior to reading (see chapter 2.6.1 on page 2-64).

Enable shaking When this item is checked, shaking is performed over

the entire incubation time. If you want to specify a
shaking time shorter than the incubation time, you have
to create two successive incubation steps (for the same
total incubation duration), one with shaking and one
without.
Frequency Shaking frequency in Hz.

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2.5.4 Dispense Steps

The D i s p e n s e dialog lets you define how the required reagents will be aspirated
and then dispensed into the various wells of the test plate (you have to specify which
wells should receive a shot).

Wrong results
All assays using multishots must be validated for their respective number!

This D i s p e n s e step is not to be used for dispensing samples and controls. For
these, refer to the P i p e t t i n g step (see chapter 2.5.1 on page 2-28). Refer also to the
P i p e t t i n g step concerning the dispensing of reagents (e. g.: diluents) into dilution
plates.

Select the D i s p e n s e item in the I n s e r t S t e p dialog (see chapter 2.5 on page 2-

26) to open the D i s p e n s e dialog.

Figure 2-21: D i s p e n s e dialog

This window shows the plate layout (see chapter 2.3.2 on page 2-20); in the default
setting all wells have a check mark. This means that all wells will receive the selected
reagent. Click on a well to remove the check mark (= deselect the dispense function);
click again to add the check mark again.

Reagent Select the reagent to be dispensed. If the desired

reagent is not yet included in this list, click on
R e a g e n t s . . . to open the Se l e c t R e a g e n t s
dialog and select or create the desired reagent (see
chapter 2.5.11.1 on page 2-59).
Volume Offset Select the volume offset for the different dispense
modes to enable the volume offset. The volume offsets
are fixed in the software and cannot be modified or
changed.

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Aspirate Check If this item is checked, the system verifies if a dive out
position is detected when retracting the tip after the
aspirate operation and if the difference between dive in
and dive out position is in accordance with the expected
drop of the liquid surface (corresponding to the
aspirated volume).
Pressure If this item is checked and pressure monitoring is
Monitoring activated in the assay header (see chapter 2.2 on page 2-
12), the air pressure in the pipetting system is monitored
during the aspirate and the data are compared with
standard values for a liquid type. This function ensures
the pipetting and dramatically reduces the risk of false
pipetting.
Liquid Type If pressure monitoring is used, a liquid type has to be
selected to obtain standard values for pressure
measurements.
Intra-well delay Define delay between individual well dispense steps in
milliseconds. This option can be used to avoid air
bubbles in the wells. However, it lengthens the dispense
time.
Volume Define the dispense volume per well in µl. The aspirate
volume will be calculated by the system:
Asp. vol.= (No. of multishots x Disp. vol.) + Oversoak
vol.
Note that the dispense volume must not be lower than
the specified minimum volume.
Ov ers o ak Define how much oversoak volume in µl is to be
aspirated (see chapter 2.5.4.1 on page 2-48).
N o . o f M u l t i s h o t s For multiple shots (fill one time, dispense several times):
number of dispense steps (see chapter 2.5.4.1 on page 2-
48).
See note above!
Back to source Volume in µl which is to be moved back into the reagent
container (see chapter 2.5.4.1 on page 2-48).
Eject tip/wash If you select this item, the pipette tip is ejected between
t i p b e t we e n each dispense step.
s ho t s Performing a multidispense step this item has not to be
used.
The wash tip option is not available since Gemini
instruments operate with disposable tips only.
Agitation Agitation time for mixing on the plate transport unit after
dispensing in seconds.
In-Well The number of I n - W e l l M u l t i s h o t s defines how
Multishots many dispense steps are executed within one well. The
volume for each in-well dispensing is calculated by the
software. The software distributes evenly the overall
volume to all dispense steps.
Wash No entries required since Gemini instrument is working
parameters with disposable tips.

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Reagents Opens the S e l e c t R e a g e n t s dialog and you can

select or enter the reagents for the dispense steps (see
chapter 2.5.11.1 on page 2-59).
Eliminate assay This option can be selected for each step defined in the
drift caused by dispense dialog of the assay.
this operation The software will calculate the time required for all
dispense steps where the option E l i m i n a t e a s s a y
d r i f t c a u s e d b y t h i s o p e r a t i o n is enabled.
The first cycle of the following wash steps is delayed
according the duration of the previous calculated
dispense time.

For more information, see chapter 2.5.1.4 on page 2-36.

Reagent Mixing Allows to mix a reagent before the dispense step will be executed.
Parameters
No. of mix Number of mix cycles for optimum mixing. A mix cycle
cycles consists of aspiration and dispensing of the liquid within
a reagent bottle.
Volume to mix Define the volume to be used for mixing.
with The volume is only considered when the N o . o f m i x
c y c l e s is not 0.
Eject tip/Wash Eject the used disposable tip (or wash the needle) after
tip after mixing mixing.
Mix between Mixes the reagent always before it will be aspirated.
shots

2.5.4.1 Multishots and Oversoak

The multi-dispense function ("multishots") is commonly used for reagents because it
shortens the dispense time and saves tips.
Oversoak defines an excess volume that will be aspirated to ensure correct
dispensing even in the last wells of a multi-dispense series. The oversoak volume is
usually defined as 10% of the total dispense volume.
Example:
If you want to dispense 50 µl of reagent per well, you can define the following
parameters:
Dispense volume = 50 µl
No. of multishots = 16
Oversoak = 80 µl (10% of 16 x 50 µl).
The pipettor will aspirate 880 µl of reagent, dispense 50 µl in the first selected 16
wells of the plate, discard the tip with the excess volume and repeat this procedure
until all the defined wells have been dispensed.
Make sure also that the total aspirate volume [(No. of multishots x Disp. vol.) +
Oversoak] does not exceed 990 µl otherwise this would exceed the syringe capacity.
However, if because of the volume offset corrections, the total volume of a multishot
step exceeds the syringe capacity, the system automatically reduces the number of
shots as required (e.g. from 16 to 14). This means that the dispense step will take a
little longer but all required wells will still be dispensed.

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If an Oversoak volume has been defined, the B ac k t o s o ur c e option lets you

select to transfer any reagent left in the pipettor after the end of a dispense operation
back to its original container. Otherwise, any excess volume left after dispensing is
discarded in the pipettor wash station before the tip is ejected. The B a c k t o
s o u r c e option is rarely used because of contamination risks.

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2.5.5 Verify Dispense Steps

If this step is inserted, the system verifies proper dispensing using the OD-value of
colored reagents. In this dialog box you have to enter the wells to be verified and the
test parameters.
A D i s p e n s e V e r i f i c a t i o n step can be included after a P i p e t t e step (for
samples and controls) or after a Dis p en se step (for reagents).

If you are running a worklist on the Gemini software in D e m o M o d e , the system

will return an error message (D i s p e n s e V e r i f i c a t i o n F a i l u r e dialog) with
an acoustic signal each time a D i s p e n s e V e r i f i c a t i o n s t e p is performed.
This is normal. Just click on the C o n t i n u e button to proceed.

In the Result Report, wells for which a dispense failure has been noted are shown at
the top of the Result Report and the corresponding samples are individually flagged
(VDFail) in the Combined report.

Select V e r i f y d i s p e n s e in the I ns er t S t e p dialog (see chapter 2.5 on page 2-

26) to open the C o l o r i m e t r i c D i s p e n s e V e r i f i c a t i o n dialog.

Figure 2-22: C o l o r i m e t r i c D i s p e n s e V e r i f i c a t i o n dialog

The plate layout you have defined with the standard setting is displayed; all wells
have a check mark, meaning that all wells are to be checked. Click on a well to
remove a check mark (= deselect verification); click again to add the check mark
again.

<= Well Value < Define the OD-value range within which the OD value of
= each well should lie. An error message is displayed if
the value determined is outside the defined range. Here
you can enter logical functions.

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Insert Function Opens the Insert function dialog and you can select the
logical functions for definition of the value range (see
query < = W e l l V a l u e <= ).
See chapter 2.8 on page 2-108
Select All All wells are selected for verification (i.e. all wells of the
plate that have a check mark). Click on the respective
well again to deselect individual wells.
Clear All Clears all checkmarks on the plate layout.

Wavelengths
Test wavelength Define the wavelength of the filter used to perform the
reading.
Ref. wavelength Define the wavelength of a possibly required reference
filter.
Relative to last If this item is enabled, the last value measured with
verification dispense verification and the current value are
compared. The value must lie within the range defined
above.

Shake
Mode Only standard mode to shake on the plate transport.
Duration Shake time.

Action on Action to take if an error occurs.

Failure
Take action if ... You have to define a limit, the exceeding of which
or more control triggers the desired action (error message or abort
wells fail assay).
Take action if ... You have to define a limit, the exceeding of which
or more sample triggers the desired action (error message or abort
wells fail assay).
Action to take Select the action to take when one of the limits defined
above has been exceeded. You may choose:
• A l e r t u s e r (error message) or
• A b o r t a s s a y.

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QA
Store mean If you select this item, the mean value of the highlighted
value in QA well is saved in the QA (Qualitative Analysis) database
database under the name of the reagent name selected here. To
view the database, select the menu item F i l e | N e w
and then in the N e w dialog the item Q . A . R e p o r t .
The Q. A. Re p or t dialog is displayed any you can
select the respective reagent. Then the course of the
reagent verification is displayed as a curve. Then the
measured value is displayed in a diagram. If this item is
enabled, you have to select the respective reagent. In
the Q . A . R e p o r t for the Reagent the verification
step values can be verified over time.
Reagent Select the reagent used. The mean values are saved in
the QA database under this name.

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2.5.6 Background Read Steps

Here you define the wavelengths to be used to measure blank plates/wells. The
value determined is then subtracted (well by well) from the reading result in the
Ba c k g r o u n d s u b t r a c t i o n step (see chapter 2.6.2 on page 2-70).
Select the item Ba c k g r o u n d r e a d in the I ns er t S t e p dialog (see chapter 2.5
on page 2-26) to open the B a c k g r o u n d R e a d dialog.

Figure 2-23: B a c k g r o u n d r e a d dialog

You can measure blank plates at certain wavelengths. The value determined is then
subtracted from the reading result.

Test wavelength Define the filter to be used for reading.

Reference Select a reference wavelength. If this item is checked,
Wavelength you can set the wavelength via the arrow buttons.

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2.5.7 Conditional Delay Steps

Select the item C o n d i t i o n a l d e l a y in the I n s e r t S t e p dialog (see chapter 2.5
on page 2-26) to open the C o n d i t i o n a l D e l a y dialog.

Figure 2-24: C o n d i t i o n a l D e la y dialog

Typically, a fixed time is defaulted for incubation, which is defined in the I n c u b a t e

dialog. In the C o n d i t i o n a l D e l a y dialog you can define a variable time period
depending on the measured value for special assays. The incubation time is finished
only when the specified measured value at the reference well has been reached and
the next step can be started.
This step is defined instead of the I n c u b a t e step.

The variable incubation time define in the Co n d i t io n a l De l a y dialog applies

only to room-temperature incubation! This incubation takes place in the photometer.

Read
Parameters
Shake Define the shake time before read in seconds.
Shake mode Select the shake mode (there is only one mode
available).
Test wavelength Define the wavelength of the filter used to perform the
reading.
Ref. Wavelength Define the wavelength of a possibly required reference
filter.
Read interval Define the read intervals in seconds (e.g. 180 = the
plate will be read every 3 minutes until the set end-of-
incubation condition is reached).
Timeout End of incubation time, even if the desired measured
value has not been reached (see explanation on W a i t
u n t i l ).

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Condition Define the end-of-incubation condition. This condition can be set either in reference
to a set OD-value or in reference to a variation of the OD-value over time (OD/minute
rate). When the set value (or rate) is reached, the incubation time is over.

Value Upon selection of this item, the incubation time is over

calculation when the OD-value entered in the W a i t u n t il edit box
mode is reached.
Rate calculation Upon selection of this item, the incubation time is over
mode when the rate entered in the W a i t u n t i l edit box (ratio
of current to previous measurement in OD/MINUTE) is
reached.
Wait until The incubation should last until the OD-value or the rate
specified here has been reached (e. g. T1 >= 1). The
entry is considered as an OD-value when the item
V a l u e c a l c u l a t i o n m o d e is enabled, or as a
rate, respective, when the item R a t e c a l c u l a t io n
m o d e is enabled. If you set the cursor into the edit
box, the I n s e r t F u n c t i o n . . . button is enabled, so
that the desired logical function can be used. See
I n s e r t F u n c t i o n dialog box (see chapter 2.8 on
page 2-108). In this edit box you may enter mathematical
operators and brackets.

Insert Opens the I n s e r t F u n c t i o n dialog box (see

Function... chapter 2.8 on page 2-108) and you can select the logical
functions for definition of the well range (see query
W a i t u n t i l).

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2.5.8 Shake Steps

Shaking is used to homogenize the contents of the wells after various dispenses or
before reading. On the Gemini instrument, a shaking function can be defined at
different stages of the process: during incubation (see chapter 2.5.3 on page 2-44), and
before reading (see chapter 2.6.1 on page 2-64).
Select the item Sh a k e in the I n s e r t S t e p dialog (see chapter 2.5 on page 2-26) to
open the S h a k e dialog.

Figure 2-25: S h a k e dialog

Duration Here you can define the duration (between 1 and 59

seconds) for shaking the microtiter plate. This shaking is
performed on the plate transport unit at ambient
temperature.
If the assay requires a longer shaking time, several
shake steps can be defined one after the other.

This shake step lets you define only the duration parameter, not the frequency as in
the incubation shaking function.

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2.5.9 Incubate Verification Steps

Incubator performance verification.

Figure 2-26: I n c u b a t e verification dialog

Verification
Index Enter the chamber number that you want to use for
incubation. This should be 0 or 1 for incubation
chambers or 0, 1 or 2 for ambient temperature
chambers.

Other Buttons All other buttons or fields of the I n c u b a t e verification dialog are identical with the
or Fields corresponding buttons or fields of the I n c u b a t e dialog (see chapter 2.5.3 on page 2-
44).

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2.5.10 Clean Washer Steps

Washer manifold maintenance. Clean the washer for 15 minutes.

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2.5.11 Reagent Database

The reagent database contains all available reagents and wash buffers.

The reagent database is available in the menu S y s t e m S e t - U p | W a s h e r,

or in the assay steps P i p e t t i n g (see chapter 2.5.1 on page 2-28), W as h (see
chapter 2.5.2 on page 2-38), and D i s p e n s e (see chapter 2.5.4 on page 2-46)!

2.5.11.1 Selection of Reagents

The reagents or wash buffers available on the system are listed in the dialog and can
be edited or selected for the assay step.

The dialog shows only reagents or wash buffers, which can be used in the assay step
(e. g. only wash buffers for the W a s h step).

Figure 2-27: Select reagents dialog

Available Shows the reagents or wash buffers defined in the

Reagents reagent database. From the reagent database you have
to transfer all reagents or wash buffers required for an
assay run to the S e l e c t e d R e a g e n t s list.
Selected Shows the reagents or wash buffer selected for the
Reagents assay step.
> Transfers the reagent or wash buffers highlighted in the
A v a i l a b l e R e a g e n t s list to the S e l e c t e d
R e a g e n t s list.
< Removes the reagent or wash buffer highlighted in the
S e l e c t e d Re a g e n t s list.
<< Removes all reagents or wash buffers available in the
S e l e c t e d Re a g e n t s list.
New... Opens the E d i t R e a g e n t D e t a i l s dialog box and
you can enter the parameters for a new reagent or wash
buffer (see below).
Edit... Opens the E d i t R e a g e n t D e t a i l s dialog box and
you can edit the parameters of the highlighted reagent
or wash buffer.

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Delete Deletes a selected reagent or wash buffer from the

reagent database.
Copy Copies a selected reagent or wash buffer and inserts it
into the reagent database with the same name plus an
index number.

2.5.11.2 Creating or Editing a Reagent

This dialog is displayed if you click the N e w . . . or E d i t . . . button in the S e l e c t
R e a g e n t s dialog.
If you have selected N e w . . . , the edit boxes contain standard values, otherwise the
previous values of the highlighted reagent or wash buffer.

Wrong results
New, modified or assumed assays must be validated to avoid wrong results.

Liquid level detection errors

New or modified reagents must be validated to avoid liquid level detection errors
(problems with low ionic strength liquids).

Several functions are not available for reagents or wash buffers! The affected
functions be disabled!

Figure 2-28: Edit reagents details dialog (e. g. add a reagent)

Name Name of reagent or wash buffer.

Type Special type of the reagent (e.g. conjugate).
The type Co n j u g a t e allows the user to apply the
conjugate grade from scanned barcode in the L o t
S p e c i f i c V a l u e s dialog.
ID ID number of reagent (barcode).

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Bottle Bottle parameters.

Properties
Volume Filling volume of the reagent bottle in ml.
Dead Vol. Dead volume of reagent bottle in ml.
Width Width/diameter of reagent bottle in mm.
Height Height of reagent bottle in mm.
Shape Select shape of reagent bottle (round or square).
Thickness Thickness of bottom of reagent bottles in mm.
Colour Color of the reagent in the load and the system status
window.

Reagent Reagent parameters.

Properties
Preparation time Enter a preparation time for the reagent in minutes.
When the reagent is needed, the system prompts you
with an acoustic signal and a message on the screen to
prepare and load the reagents.
Lasts for the If this item is checked, the reagent can be used for the
duration of a entire duration of the worklist.
worklist
Lifetime Enter a life time for the reagent in minutes. When the
reagent would be needed a second time, and the
lifetime is elapsed after loading the reagent, the
software prompts the user to remove and load a new
reagent bottle
Allow changing Allow to change bottles during processing the same
of bottles during plate.
a dispense

Reagent Define the desired aspirate and dispense profiles, which are pre-defined in the
Dynamics U t i l i t i e s | S y s t e m S e t u p menu on the P i p e t t e tab.

Aspirate profile Select the aspirate profile. The name of the selected
profile is displayed.
Dispens e pr ofile Select the dispense profile. The name of the selected
profile is displayed.

Wrong results
It is necessary to use only validated assay/profile combinations to avoid wrong
results.

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Use appropriate profiles

It is very important for precise and reliable pipetting and dispensing of the reagents
to select appropriate profile!

Define the desired aspirate and dispense profiles, which are pre-defined in the
U t i l i t i e s | S y s t e m S e t u p menu on the P i p e t t e tab.
Click on Add or E d i t button the enter/change the profiles for assigned volume
values.

Maximum Shows the maximum volume for the used aspirate and
volume dispense profiles
Aspirate profile Select the aspirate profile. The name of the selected
profile is displayed.
Dispense profile Select the dispense profile. The name of the selected
profile is displayed.

Wrong results
It is necessary to use only validated assay/profile combinations to avoid wrong
results.

Use appropriate profiles

It is very important for precise and reliable pipetting and dispensing of the reagents
to select appropriate profile!

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2.6 Read Definition

The evaluation is programmed by adding individual evaluation steps to a reader step.

Default Steps A new assay contains three default steps:

Reader settings Definition of photometer parameters (see chapter 2.6.1 on

page 2-64).
Background Subtraction of background value (see chapter 2.6.2 on
subtraction page 2-70).
Report Settings Definition of result output (see chapter 2.6.3 on page 2-73).

Insert It is possible to insert further evaluation steps (see chapter 2.7 on page 2-86).
Evaluation
Steps

Editing Assay Double-click on the respective symbol in the assay tree to open the respective
Steps parameter window.

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2.6.1 Reader Settings

Double-click with the left mouse button on the R e a d e r s e t t i n g s symbol in the
assay tree to open the C o l o r i m e t e r S e t t i n g s dialog.

2.6.1.1 Endpoint Tab

Figure 2-29: C o l o r i m e t e r S e t t i n g s dialog - E n d p o i n t tab

Wavelengths Define the wavelengths.

Test wavelength Define the wavelength of the filter used to perform the
reading. You can set the wavelength via the arrow
buttons.
Ref. wavelength Define the wavelength of a possibly required reference
filter. If this item is checked you can set the wavelength
via the arrow buttons.

Shake Shake parameters prior to reading.

Mode Select the shake mode (there is only a standard mode

available).
Duration Define the shake duration in seconds.

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Multi- Parameters for 2nd reading using a different wavelength, when the results of the first
Wavelength reading were outside the reading range.
Reading
Enabled If this item is checked you can define the wavelength
used for the 2nd reading. A 2nd reading takes place only
when the results of the first reading were outside the
reading range.
Secondary test Select a filter wavelength for the 2nd reading. If this item
wavelength is checked you can set the wavelength via the arrow
buttons.
Secondary Select a reference filter wavelength for the 2nd reading.
reference If this item is checked you can set the wavelength via
wavelength the arrow buttons.

Data Select the data conversion mode for both readings.

Conversion
Mode
Linear Linear regression to recalculate to the original filter.
Regression
F or m ul a Specify a factor to be used for multiplication of the result
in order to get to the result of the reading with the first
filter pair. The formula may include: labels, digits,
mathematical operators, brackets and the functions that
can be called via the item I n s e r t F u n c t i o n . . ..
Insert Opens the I n s e r t F u n c t i o n dialog box (see
Function... chapter 2.8 on page 2-108) and you can select the logical
functions for conversion of the reading results (see
query F o r m ul a).

Out Of Range The default OVER limit and replacement in the system setup can be overwritten for
Values each individual assay.

Use reader Activate this option to use the reader defaults (see
defaults System-Set-up / Colorimeter tab).
OVER limit Enter the upper limit value (OD) for the photometer (e.g.
2.5). For more details see instrument specifications.
Enabled You can select if another character string is to be output
instead of the measured value when the result is above
or below the limit value, e.g. a digit or a comment. Click
on the respective check box to enable the respective
edit box and you can make your entry.
OVER When exceeding the value: [...] should be printed
replacement instead of the OVER text (2.5).
v al u e
UNDR When falling short of the value: [...] should be printed
replacement instead of the UNDER text.
v al u e

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2.6.1.2 Layout Tab

Figure 2-30: C o l o r i m e t e r S e t t i n g s dialog - L a y o u t tab

Layout Definition of the result output.

Display Header If checked, any "header" information is displayed, e.g.

data model formulae.
Body: Matrix Result display as matrix (see information in the M a t r i x
box).
Body: Table Result display as table (see information in the T a b l e
box).
Display Legends If checked, any legends are displayed, e.g. user-defined
annotations.

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Matrix Select which results are to be output in the form of a matrix.

Available Fields Available fields:

• Sample ID
Identification number of sample.
• Sample name
Name of the sample
• Sample Location
Position of the sample in the rack.
• Well Location
Position of the sample on the microtiter plate.
• Layout Label
Label used for well type (e. g. T, B, NC ...).
• Input: Data
Values that go into the processing option. e.g. OD.
• Input: Mean
Mean Values that go into the processing option e.g.
OD.
• Input: SD
Standard deviation of input
• Input: CV
Coefficient of variation of input
• Input: SE
Standard error of input.
• Output: Data
Values that come out of the processing option.
• Output: Mean
Mean of values that come out of the processing
option.
• Output: SD
Standard deviation of output.
• Output: CV
Coefficient of variation of output.
• Output: SE
Standard error of output.
• Flag
Sample related messages
Copy the respective parameters with the arrow buttons
> or >> to the S e l e c t e d F i e l d s list. You can
change the order via the M o v e U p and M o v e
D o w n buttons according to your needs.
Selected Fields List of selected parameters which are output after
reading in form of a matrix (see also A v a i l a b l e
F i e l ds).
> Copies the highlighted parameters from the
A v a i l a b l e F i e l d s list to the S e l e c t e d F i e l d s
l i s t.
>> Copies all parameters from of the A v a i l a b l e
F i e l ds list to the S e l e c t e d F i e l d s list.

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< Removes the highlighted parameters from the

S e l e c t e d F i e l d s list.
<< Removes all parameters from the S e l e c t e d F i e l d s
list.
Move Up Moves the highlighted parameter in the Se l e c t e d
F i el d s list up one row.
Move Down Moves the highlighted parameter in the Se l e c t e d
F i el d s list down one row.
Font... Opens the F on t dialog box and you can define font,
size and type for data output. The default font is Arial,
10pt, standard. The selected font is valid for matrix as
well as for table presentation.
Gridlines Select this item to show gridlines.

Calculations Calculation parameters.

Use Averaged Select this item to use averaged input values.

Inputs
Averaging Mode Select the average mode: Ar it h m e t i c M e a n ,
G e o m e t r i c M e a n or M e d i a n .

Table Select which results you want to output in a table: this is the same parameter
selection as in the M a t r i x area. Proceed in the same manner: Using the arrow
buttons, copy the desired parameters to the S e l e c t e d F i e l d s list. Click
F o nt . . . in the M a t r i x area to select another font and change the defaulted font
parameters.

Column Title Enter a column title for each column.

Column Width Define the column width for each column.
T y p e O r de r Define the order of the well types for data output. Set the
mouse pointer on the well type you want to move. Push
the left mouse button and move the well type up or down
with mouse button held down. The well type is
positioned in the list at the point where you release the
mouse button.

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Scientific Controls when numbers are displayed in scientific format and when they aren't.
Format
Auto Auto format. You can select the number size (small,
intermediate, large)
• If S m a l l N u m b e r s is checked then any values
less than 1.0 are displayed in scientific format.
• If I n t e r m e d i a t e N u m b e r s is checked then
values between 1.0 and 10000.0 are displayed in
scientific format.
• If L a r g e N u m b e r s is checked then any values
above 10000.0 are displayed in scientific format.
Fixed Exponent Presentation with fixed exponent. Set the value by
clicking on the arrow buttons. For example: 3 means x
103.
Exponent Presentation with multiple exponents. Set the value by
Multiple clicking on the arrow buttons. For example: 3 means x
103.
Decimal Place Define the decimal place. For example: 3 means 1.000.

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2.6.2 Background Subtraction

In the assay tree, double-click with left mouse button on the B a c k g r o u n d
S u b t r a c t i o n symbol to open the B a c k g r o u n d Su b t r a c t i o n dialog.

Figure 2-31: Background subtraction dialog

To disable this step, select N o n e in the B a c k g r o u n d S u b t r a c t i o n M o d e

drop-down menu.
B-wells are those cavities which are subtracted as blank value from the other wells.
Background calculation takes place depending on the selected mode.

Background Select the calculation method for the blank value:

Subtraction • None
Mode No background subtraction. This step is disabled.
• Average
The average of the B-wells is subtracted from each
individual well, which is identified by a check mark.
• Row
The B-well in a certain row is subtracted as
background from the wells in that row.
• Column
The B-well in a column is subtracted as background
from the wells in that column.

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• Paired
Paired subtraction of the background (B) from the
other wells. The reverse order of the categories on
the plate is used. This means: B1 is subtracted from
the first sample of the last category (e.g. T), B2 from
the 2nd sample of the last category, etc. If all
samples of the last category have been calculated in
this manner, the next B-value is subtracted from the
first samples of the second to last category. The last
B-value is then subtracted from the last sample of the
first category.
Example: Samples are arranged on a plate as
follows:
CO1 B1
CO2 B2
PC1 B3
PC2 B4
T1 B5
T2 B6
In this case, B1 is subtracted from T1, B2 from T2,
B3 from PC1, B4 from PC2, B5 from CO1 and B6
from CO2 (see also result file *.res).
• Plate
A background value which has been saved to a file
can be subtracted for the entire plate. The file is
called via the P l a t e I D browser or chosen before a
run as L i n k e d P l a t e I D .
If the results of the linked or specific plate can not be
found, the software shows an error messages and no
background subtraction will be performed.
• P r e v i o u s Va l u e
The average of the B-Wells of the last processed
Av er age blank mode assay is used for
background subtraction.
Due to the limited traceability of the P r e v i o u s
V a l u e, this function should not be used.
See note below!
• Custom
In this mode you can assign B-wells to the T-wells. If
you select this mode, the B-wells are automatically
listed in the menu next to the well matrix. First select
a B-well in the menu and then the other well in the
matrix from which the B-well is to be subtracted.
Proceed in the same manner with all B-wells.

Wrong result
Do not use the calculation method P r e v i o u s Va l u e when assay layout does not
contain a blank.

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Plate This item is enabled only if you have selected P l a t e in the previous query.
Subtraction
Mode
Plat e I D Define the file name of the plate ID.
Browse Opens the Open dialog box for selection of a result
file.
Use Linked Allows the user to choose another plate with the
Plat e I D background values before a run.

Multi-Reading Options for the kinetics mode.

Mode
Subtract From Background value subtraction only from final result.
Final Result
Subtract From Background value subtraction from each individual well
Individual result.
Readings

Paired/Custom The microtiter plate layout is displayed and in Cu s t om mode those wells from
Subtraction which the background is to be subtracted are identified by a check mark.
Mode

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2.6.3 Report Settings

In the assay tree, double-click with the left mouse button on the R e p o r t
S e t t i n g s folder. The R e p o r t S e t t i n g s dialog is displayed.

2.6.3.1 Report Tab

On the tab R e p o r t you select the data fields to appear in the result printout. The
layout of the individual components is defined in the respective dialogs.

Figure 2-32: R e p o r t S e t t i n g s dialog - R e p o r t tab

Page Header/ The report page header and page footer can be defined by any entries as well as by
Footer the following place holders:
• & D = date
• & F = name of result file
• & I = lab
• & Q = quality control
• & P = page number
• & S = system serial number
• & V = user software version number
The header/footer is printed on each page of the report.

L e f t, C e n t r e, In the header you can make entries in 3 separate areas:

Right left, centre and right.

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Report The structure of the report is defined by the individual data fields and their order.
Structure Copy the desired data fields from the A v a i l a b l e F i e l d s list to the S e l e c t e d
F i e l ds list and change their order as needed.

Clearly arranged result report

Include all process related information (e. g. flags, general process messages and
plate related events) in the result output!

Available Fields Shows the available data fields of a report:

• Laboratory Details
Laboratory name, address, etc.
• Assay Header
Path of test definition, wavelengths used, date/time
read, operator.
• Lot Specific Values
Lot specific data as entered in the L o t S p e c i f i c
V a l u e dialog.
• Incubation Results
Detailed information regarding incubation time and
incubation temperature for each individual incubation
step.
• Events
Error messages and messages about user
interactions taken from the event log.
• Reader Results
Data specified in the R e a d e r S e t t i n g s layout
menu.
• Validation Criteria
Data specified in the V a l i d a t i o n C r i t e r i a step.

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• Spreadsheet Results 1
Data specified in the S p r e a d s h e e t layout menu
1.
• Spreadsheet Results 2
Data specified in the S p r e a d s h e e t layout menu
2.
• Spreadsheet Results 3
Data specified in the S p r e a d s h e e t layout menu
3.
• Qualitative Results
Data specified in the Q u a l i t a t i v e layout menu.
• Q u a nt i t at i ve R es u l t s1
Data specified in the Q u a n t i t a t i v e S e t t i n g s
1 layout menu.
• Q u a nt i t at i ve R es u l t s2
Data specified in the Q u a n t i t a t i v e S e t t i n g s
2 layout menu.
• Combined Report
Data specified in the R e p o r t S e t t i n g s
C o m b i n e d R e p o r t menu.
• <Page Break>
Insert of a new page during printout.
Selected Fields Shows the data fields of the reports selected via the
arrow buttons.
> Copies the data fields highlighted in the A v a i l a b l e
F i e l ds list to the S e l e c t e d F i e l d s list.
>> Copies all data fields to the S e l e c t e d F i e l d s list.
< Removes the data fields highlighted from the
S e l e c t e d F i e l d s list.
<< Removes all data fields from the Se l e c t e d F i e l d s
list.
Move Up Moves the data field highlighted in the list up one row.
Move Down Moves the data field highlighted in the list down one row.

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2.6.3.2 Combined Report Tab

With the combined report option a report can be created which includes the result of
all data processing steps in one table or/and one matrix. In the window shown bellow
the settings for this individual report can be entered.

Figure 2-33: R e p o r t S e t t i n g s dialog - C o m b i n e d R e p o r t tab

Layout Definition of the result output.

Display Header If checked, any "header" information is displayed, e.g.

data model formulae.
Body: Matrix Result display as matrix (see information in the M a t r i x
box).
Body: Table Result display as table (see information in the T a b l e
box).
Display Legends If checked, any legends are displayed, e.g. user-defined
annotations.

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Matrix Select which results are to be output in the form of a matrix.

Clearly arranged result report

Include all process related information (e. g. flags, general process messages and
plate related events) in the result output!

Available Fields Available fields:

• Sample ID
Identification number of sample.
• Sample name
Name of the sample
• Sample Location
Position of the sample in the rack.
• Well Location
Position of microtiter plate.
• Layout Label
Label used for well type (e. g. T, B, NC ...).
• Flag
Sample related messages
• Barcode
Barcode of each multi-preparation sample tube. Only
for multi-preparation assay.
• Result history
Initial result for the sample (for cases where the
sample is being retested).
• Raw value
OD value (before background subtraction)
• Raw mean
Average OD value (before background subtraction)
of every single measurement
• Raw SD
Standard deviation of raw value
• Raw CV
Coefficient of variation of raw value
• Raw SE
Standard error of raw value
• Reader value
OD value (after background subtraction)
• Reader mean
Average reader value of replicates
• Reader SD
Standard deviation of reader value
• Reader CV
Coefficient of variation of reader value
• Reader SE
Standard error of reader value

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• Reader 2 value
OD value (after background subtraction)
• Reader 2 mean
Average reader value of replicates
• Reader 2 SD
Standard deviation of reader value
• Reader 2 CV
Coefficient of variation of reader value
• Reader 2 SE
Standard error of reader value
• Spread. 1 value
Result of spreadsheet 1 calculation
• Spread. 1 mean
Average of the replicates after spreadsheet 1
calculation
• Spread. 1 SD
Standard deviation of spreadsheet 1 value
• Spread. 1 CV
Coefficient of variation of spreadsheet 1 value
• Spread. 1 SE
Standard error of spreadsheet 1 value
• Spread. 2 value
Result of spreadsheet 2 calculation
• Spread. 2 mean
Average of the replicates after spreadsheet 2
calculation
• Spread. 2 SD
Standard deviation of spreadsheet 2 value
• Spread. 2 CV
Coefficient of variation of spreadsheet 2 value
• Spread. 2 SE
Standard error of spreadsheet 2 value
• Spread. x ...
x: calculation/value - see above
• Quant. 1 value
Result of first quantitative step
• Quant. 1 mean
Average value for the replicates after quantitative
step one
• Q u a n t . 1 SD
Standard deviation of result of quantitative 1
• Q u a n t . 1 CV
Coefficient of variation for result of quantitative 1
• Q u a n t . 1 SE
Standard error of result for quantitative 1
• Qual. value
Qualitative result of replicate of sample.
• Qual. mean
Qualitative result of average of the sample replicates.

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• Quant. 2 value
Result of second quantitative step
• Quant. 2 mean
Average value for the replicates after quantitative 2
• Quant. 2 SD
Standard deviation of result of quantitative 2
• Quant. 2 CV
Coefficient of variation for result of quantitative 2
• Quant. 2 SE
Standard error of result for quantitative 2
Copy the respective parameters with the arrow buttons
> or >> to the S e l e c t e d F i e l d s list. You can
change the order via the M o v e U p and M o v e
D o w n buttons according to your needs.
Selected Fields List of selected parameters which are output after
reading in form of a matrix (see also A v a i l a b l e
F i e l ds).
> Copies the highlighted parameters from the
A v a i l a b l e F i e l d s list to the S e l e c t e d F i e l d s
l i s t.
>> Copies all parameters from of the A v a i l a b l e
F i e l ds list to the S e l e c t e d F i e l d s list.
< Removes the highlighted parameters from the
S e l e c t e d F i e l d s list.
<< Removes all parameters from the S e l e c t e d F ie l d s
list.
Move Up Moves the highlighted parameter in the S e l e c t e d
F i e l ds list up one row.
Move Down Moves the highlighted parameter in the S e l e c t e d
F i e l ds list down one row.
Font... Opens the F on t dialog box and you can define font,
size and type for data output. The default font is Arial,
10pt, standard. The selected font is valid for matrix as
well as for table presentation.
Gridlines Select this item to show gridlines.

Calculations Calculation parameters.

Use Averaged Select this item to use averaged input values.

Inputs
Average Mode Select the average mode: A r i t h m e t i c M e a n ,
G e o m e t r i c M e a n or M e d i a n .

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Table Select which results you want to output in a table: this is the same parameter
selection as in the M a t r i x area. Proceed in the same manner: Using the arrow
buttons, copy the desired parameters to the S e l e c t e d F i e l d s list.

Column Title Enter a column title for each column.

Column Width Define the column width for each column.
T y p e O r de r Define the order of the well types for data output. Set the
mouse pointer on the well type you want to move. Push
the left mouse button and move the well type up or down
with mouse button held down. The well type is
positioned in the list at the point where you release the
mouse button.

Scientific Controls when numbers are displayed in scientific format and when they aren't.
Format
Auto Auto format. You can select the number size (small,
intermediate, large)
• If S m a l l N u m b e r s is checked then any values
less than 1.0 are displayed in scientific format.
• If I n t e r m e d i a t e N u m b e r s is checked then
values between 1.0 and 10000.0 are displayed in
scientific format.
• If L a r g e N u m b e r s is checked then any values
above 10000.0 are displayed in scientific format.
F i x e d Ex p o n e n t Presentation with fixed exponent. Set the value by
clicking on the arrow buttons. For example: 3 means x
103.
Exponent Presentation with multiple exponents. Set the value by
Multiple clicking on the arrow buttons. For example: 3 means x
103.
Decimal Place Define the decimal place. For example: 3 means 1.000.

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2.6.3.3 Export Tab

On this tab you define the parameters for export of the report data.

Figure 2-34: R e p o r t S e t t i n g s dialog - E x p o r t tab

Available Data The Text File format, the C S V format or the

F or m at s A S T M E 1 3 9 4 format is available as data format. If
you want to export the report select the item and click
the > button. The data format is copied to the
S e l e c t e d Da t a F o r ma t s list. Now click on the
S e t t i n g s . . . button to define the structure of the data
format.
See also:.
• T e x t F i l e S e t t i n g s dialog box (see
chapter 2.6.3.4 on page 2-82) for T ex t F i l e format
and the CSV format.
• A S T M E 1 3 9 4 E x p o r t dialog box (see
chapter 2.6.3.5 on page 2-84).
Selected Data Shows the selected data formats.
F or m at s
> Copies the highlighted data format from the
A v a i l a b l e D a t a F o r m a t s list to the S e l e c t e d
Data Formats.
< Removes the highlighted data format from the
S e l e c t e d Da t a F o r ma t s list.
<< Removes all data formats from the S e l e c t e d D a t a
F o r m at s list.
Settings Opens the T e x t F i l e S e t t i n g s dialog box (see
chapter 2.6.3.4 on page 2-82) or the A S T M E 1 3 9 4
E x p o r t dialog box (see chapter 2.6.3.5 on page 2-84).

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2.6.3.4 Text File Settings

In this dialog you define the structure of the export file:
Define the desired headers and data fields as well as the separator between the
individual data and select the format (table/matrix).
For the CSV (Comma-Separated Values) format, several Data Fields will be
preselected.

Figure 2-35: Definition of the report file parameters

Available Shows the available header fields of a report:

Header Fields • Assay Header
Export data about the run (e. g. date, operator etc.).
• Kinetic Readings
Data specified in the R e a d e r S e t t i n g s layout
menu (kinetic assay protocol type)
• Validation Criteria
Data specified in the V a l i d a t i o n C r i t e r i a menu
• Qualitative
Data specified in the Q u a l i t a t i v e layout menu
• Quantitative
Data specified in the Q u a nt i t at i ve S et t i ng s
layout menu
• LIS Assay
Assay name as known to the LIS (see ASTM assay
link feature).
Selected Header Shows the selected header fields.
F i el d s
Available Data Shows the available data fields of the export file:
F i el d s This is the same parameter selection as in the M a t r i x
area of the C o m b i n e d R e p o r t T a b (see page 2-
76).
Selected Data Shows the selected data fields for the report.
F i el d s

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> Copies the highlighted parameters from the

A v a i l a b l e F i e l d s list to the S e l e c t e d F i e l d s
l i s t.
>> Copies all parameters from of the A v a i l a b l e
F i e l ds list to the S e l e c t e d F i e l d s list.
< Removes the highlighted parameters from the
S e l e c t e d F i e l d s list.
<< Removes all parameters from the S e l e c t e d F ie l d s
list.
Move Up Moves the highlighted parameter in the S e l e c t e d
F i e l ds list up one row.
Move Down Moves the highlighted parameter in the S e l e c t e d
F i e l ds list down one row.
Separator Enter the desired delimiter separating the individual data
from each other, e.g. colon (;).
F or m at Define the formats in which the data will be output: you
may choose T a b l e or M a t r i x . The respective
column and row titles are indicated.
Title Here you may enter another title for the field names
displayed in the S e l e c t e d D a t a F i e l d s list. The
new title is used in the export file.
Proceed as follows: In the S e l e c t e d D a t a
F i e l ds list, highlight the field name you want to edit for
the report file. This name is then displayed in the Title
edit box. Overwrite the displayed name. The new name
is then automatically used for the export file.

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2.6.3.5 ASTM E 1394 Export

Figure 2-36: ASTM E 1394 export dialog

In this dialog you define the structure of the ASTM E 1394 export:

Results Shows the selected data fields for the ASTM E 1394
export.
Export Control If this item is checked, the values of the control wells are
Well Values also included in the export file.
Identifier For each result specify an ID which will be appended to
the universal test ID field of the result record.
Result Shows the available data fields for the ASTM export
record:
• Reader mean
Average OD value of replicates.
• Qual. mean
Qualitative result of average of the sample replicates.
• Quant.1 mean
Average quantitative 1 value of replicates.
• Spread.1 mean
Average spreadsheet 1 value of replicates.
• Quant.2 mean
Average quantitative 2 value of replicates.
• Spread.2 mean
Average spreadsheet 2 value of replicates.
• Spread.3 mean
Average spreadsheet 3 value of replicates.
• Spread.4 mean
Average spreadsheet 4 value of replicates.
• Reader 2 mean
Average reader 2 value of replicates.

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Mean / R e p l i c a t e These options apply to replicate wells of the same

sample.
If you select M e a n, the values exported are the mean
values as selected in the Re s ult drop-down list. If you
select R e p l i c a t e , although mean values are selected
in the R e s u l t drop-down list, the values exported will
be the individual values for each replicate.
For example, if you want the ASTM export data to
include the Reader value of each 6 replicates of a
sample (and NOT the mean value):
1. In the Result drop-down list, select "Reader mean".
2. Click Ad d . In the Results list on the left, you can
now see "Reader value" (and NOT "Reader mean").
3. Now select "2" in the entry field next to the Replicate
option and click Add again.
4. Repeat this last step for replicates 3, 4, 5 and 6.
5. Click O K twice to close the dialog boxes and go
back to the assay.

The selected mean and/or replicate values are listed at

the end of the Report settings section of the assay.
Move Up Moves the highlighted parameter in the R e s u l t s list
up one row.
Move Down Moves the highlighted parameter in the R e s u l t s list
down one row.
Add Add new parameter to the R e s u l t s list.
Delete Delete selected parameter form the R e s u l t s list.
Clear Clear the R e s u l t s list.

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2.7 Evaluation Definition

The evaluation is programmed by adding individual evaluation steps.

Wrong results
Because of mathematical roundings it is necessary to validate assays!

Insert Click with the right mouse button on R e a d e r s e t t i n g s or R e p o r t S e t t i n g s

Evaluations in the assay tree (see figure 2-5: on page 2-7) and then select I ns er t S t e p in the
Steps menu window. The I n s e r t S t e p dialog is displayed, showing the evaluation steps
you can select.

Figure 2-37: I n s e r t S t e p dialog

Validation Inserts a validation criteria step (see chapter 2.7.1 on

criteria page 2-87).
Qualitative Inserts a qualitative analysis step (cutoff) (see
Settings chapter 2.7.2 on page 2-89).
Quantitative Inserts an quantitative analysis step (e.g. standard curve
Settings evaluation, correction of reading value, alpha method)
(see chapter 2.7.3 on page 2-93).
Spreadsheet Inserts a spreadsheet step (mathematical calculations to
the results) (see chapter 2.7.4 on page 2-106).

After selection of a step the respective dialog is displayed for parameter entry. Once
you have entered your parameters and saved your entries, the new step is inserted
in the assay tree.

Order of You can arrange the individual steps in any order. The order is defined during new
Evaluation definition of a step by clicking with the right mouse button on the symbol before the
Steps one you the want to place the new steps.
Each evaluation step uses the output data of the previously programmed evaluation
step. The evaluation step Q u a n t i t a t i v e S e t t i n g s can be selected twice, all
other steps only once.

Editing Assay Double-click on the respective symbol in the assay tree to open the respective
Steps parameter windows.

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2.7.1 Validation Criteria (V. C.)

Here you can introduce conditions for quality control using equations. These
equations allow you to specify criteria for the test. If these criteria are not met, you
may choose to abort the evaluation of the results.

Figure 2-38: V a l i d a t i o n C r i t e r i a C h e c k dialog

V.C. Check Edit box for new functions.

Insert Function Opens the I n s e r t F u n c t i o n dialog box and you can
select a logical link for the description of your conditions
(see chapter 2.8 on page 2-108).
New Click this button to enable a new row and to enter
another equation.
Delete Deletes the row highlighted in the menu.
Clear All Clears all characters available in the menu.
Undo Revokes the previous action.
Redo Revokes the undo function.
Report Format Select the information the report should contain.
• Detailed (All)
All QC data (equations, values, etc.) are included in
the results report.
• Detailed (Failures Only)
Only the QC equations that fail are reported.
• Descriptive (Failures Only)
Only an error message without further explanation is
displayed.
• None
An error will not be reported.
Don’t evaluate If this box is checked as soon as a validation criteria is
results if not fulfilled no results will be displayed because the run
Validation is invalid.
Criteria fails

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Examples:
The mean of the positive controls must be above 0.7 OD:
PC>0.7.

Each of the negative controls must be within 50% of the mean:

0.5*NC<=NCi<=1.5*NC

Two negative controls must be valid:

Valid(NC)>=2

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2.7.2 Qualitative Evaluation

Here you can define the parameters for qualitative evaluation of the results. Click
Qu a l i t a t i v e Se t t i n g s in the I n s e r t S t e p dialog to open the Q u a l i t a t i v e
S e t t i n g s dialog.

2.7.2.1 Typing Tab

Here you enter the parameters for qualitative evaluation.

Figure 2-39: Q u a l i t a t i v e S e t t i n g s dialog - T y p i n g tab

Use Stored If this item is checked, all other items on this tab are
Control Value dimmed. In this case, enter the name of the file including
File the control values.
Browse Select the stored control value file.
Histogram of Select a result histogram.
results

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Conditions Define the conditions for evaluation.

If In this field you enter the condition, e.g.

'Sample<NC+0.05'. It is automatically entered in the first
row (or in case several rows exist in the highlighted row)
of the list below.
Input terms: This formula has to include 'Y', 'Sample' or
'Sample.n' once (n = individual value of well). Moreover,
this edit box may contain: well labels, digits,
mathematical operators and brackets, as well as the
functions offered via I n s e r t F u n c t i o n . . . .
then Result := Select the equation respective evaluation: positive +,
negative - or equivocal ? . This information is
automatically inserted in the highlighted row of the list of
conditions.
List of conditions The conditions are listed, e.g. If
'Sample>=NC+0.05',Then Result = '+'.
Insert Function Opens the I ns er t F u nc t i o n dialog box and you can
select a logical link for the description of your conditions
(see chapter 2.8 on page 2-108).
Add Click this button to create a new row in the list for
another condition. The new row starts with "If..." You can
define a condition via keyboard or by clicking the
I n s e r t F u n c t i o n . . . button.
Remove Removes the highlighted condition from the list of
conditions.
Clear Clears the entire list of conditions.
Move Up Moves the highlighted row in the list of conditions up one
row.
Move Down Moves the highlighted row in the list of conditions down
one row.
Default Result Results that do not match the specified conditions are
identified by the sign to be chosen in this box. You may
choose +, - and ? .

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Grey Zones Define grey zones, i.e. reading ranges which are not assigned to any result type.

Zones Number of zones.

Low expression Low expression of grey zone. You can enter well labels,
digits, mathematical operators, brackets and functions.
High expression High expression of grey zone. Input options as for L o w
e x p r e s s i o n.
F on t Select fonts.

Result Types Describe the result types, i.e. enter the explanation for the characters +, - and ? .

Result Enter the result type (+, - , ? ). It is automatically entered

in the first row of the legend list or if several legend rows
exist in the highlighted row.
Legend Here you enter the description for the result type.
Separated by a tab, the description is written in the
same row as the result type.
List of legends Shows the defined result types with description
(separated by a tab stop) which were entered in the two
edit boxes above.
Add Adds a new row for result and legend.
Remove Removes the highlighted row from the legend list.
Clear Clears the legend list.
Move Up Moves the highlighted row in the legend list up one row.
Move Down Moves the highlighted row in the legend list down a row.

Notes Enter comments explaining the abbreviations.

Note The additional information entered here appears on the

printout of the result report. The input is automatically
entered in the menu above with an equal sign.
Expression Enter the expression (abbreviation) you want to explain.
This information is automatically entered in the menu
behind the equal sign.
List of notes Shows the defined notes which were entered in the two
edit boxes above.
Add Click on Add to insert an additional row with
explanation.
Remove Removes the highlighted row.
Clear Clears all notes in the N o t e s group box.

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2.7.2.2 Other Tabs

All other tabs of the Q u a l i t a t i v e S e t t i n g s dialog are identical with the
corresponding tabs of other dialogs:
• Validation Criteria (V. C.) (see chapter 2.7.1 on page 2-87)
• Annotation Tab (see chapter 2.7.3.7 on page 2-102)
• Layout Tab (see chapter 2.6.1.2 on page 2-66)
• Retest Tab (see chapter 2.7.3.9 on page 2-104)

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2.7.3 Quantitative Evaluation

Select Q u a n t i t a t i v e S e t t i n g s in the I n s e r t S t e p dialog to open the
Qu a n t i t a t i v e S e t t i n g s dialog.

2.7.3.1 Data Model Tab

Figure 2-40: Q u a n t i t a t i v e S e t t i n g s dialog - D a t a M o d e l tab

Data Model Select the data model. You may choose:

• Linear Regression
y = a + bx.
Fits a straight line model through the data points
using the "least-squares" method.
• Quadratic Regression
y = a + bx + cx2.
Fits a quadratic curve model through the data points
using the "least-squares" method.
• Cubic Regression
y = a + bx + cx2 + dx3.
Fits a cubic curve model through the data points
using the "least-squares" method.
• Quartic Regression
y = a + bx + cx2 + dx3 + ex4
Fits a quartic curve through the data points using the
"least-squares" method.

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• Robust Linear Regression

y = a + bx
Fits a straight line through the data points by
minimizing the absolute deviation of the points from
the line.
• Cubic Spline
y = a0 + a1x + ∑bjΦj(x)
Fits a series of smooth cubic curves through the data
points.
• Akima
Fits a series of piece wise cubic curves through the
data points.
• Point-Point
Joins adjacent data points using a straight line.
• 4-Parameter
y=(A-D)/(1+((x/C)B))+D
Fits an S-shaped curve through the data points.
• Michaelis-Menten
y = Vmax x / (x + Km)
This model simulates the catalytic activity of an
enzyme. This equation is solved using the
Lineweaver-Burk transformation.
• U s e r - De f i n e d
If you select this item the U s e r - D e f i n e d
M o d e l field is enabled. Here you can enter
calculation formulae e.g. for correction of the
measured value or the Alpha method. A weighted
SD calculation is not possible here.
• Stored Model
If you select this item the S t o r e d M o d e l F i l e
N a m e field is enabled. Enter the name of the file
containing the curve you want to use for calculation
of the current plate results. No weighted SD
calculation is possible. Instead of a fixed file you can
allow, that the user could select a plate (linked plate
ID) before the run.
Result Units Define the result units, e.g. Titer, IU/ml.
SD weighted Some data models have the option of weighting the
data model importance of the data model by using the standard
deviation of the replicates that were averaged to
produce that data point (e.g. Linear Regression, 4-
parameter). The model will fit its line/curve closer to
points with a lower SD.
Display ANOVA ANOVA stands for ANalysis Of VAriance. This is a table
table which describes various sources of errors relating to the
data model. This produces t-values (and probabilities)
for each coefficient and a F-value for the fit as a whole.
These can be used to determine just how good the fit is
to the data.

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Display For the standards, the actual concentration

predicted corresponding to their measured OD values is
standard values displayed. These are calculated based on the curve
equation which is determined using the curve fit.
Merge results This will replace any currently invalid results with valid
with previous results from the previous quantitative step. Valid results
d a t a mo d e l are left unchanged. This effectively merges the results
from the two quantitative steps.
Model The button is enabled only if you select the item 4-
Parameters Parameter in the D a t a M o d e l menu. With this data
model you have to define 4 parameters that define the
curve.
Press the button to open the 4 - P a r a m e t e r F i t
O p t i o n s dialog.

• Auto
In this column you can define for each of the 4
parameters - by clicking on the respective check box
- if it is to be defined automatically (Auto) or if user
wants to enter a known value. A check mark in the
check box means automatic definition of the
parameters. Deselect the check mark to enable the
respective edit box for entry.
• Max. no. of iterations
Enter the number of iterations for curve calculation to
be performed by the program to fit the curve.
• Report values below A as 0.000
In the Quantitative Settings, the data model 4-
Parameter allows to replace values to “0.000” in
case the calculated value is lower than the
parameter “A”. The replaced value of “0.000” will be
used for further calculations. This replacement
applies to all well types (including standards if the
D i s p l a y p r e d i c t e d s t a n d a r d v a l u e s box
is checked).

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Percentage Define percentage mode.

Mode
Percentage Y Scaling in percent by defining a 0% and a 100% value.
Click on the check box if you want to use this mode. This
enables the next 3 edit boxes.
0% Value Enter the 0% value. Enter it as minimum value of one of
the measured samples in the following notation:
MIN(well type). Here you may enter: well labels, digits,
mathematical operators and brackets.
100% Value Enter the 100% value. Enter it as maximum value of one
of the measured samples in the following notation:
MAX(well type). Here you may enter: well labels, digits,
mathematical operators and brackets.
Report LC/LD Enter the percentage of the lethal dose. This is drawn
into the diagram as a line, allowing visual control of the
reading results.

Data You can choose between logarithmic and linear presentation of the X or Y axis.
Transformation

Standards In this range you have to define the standard values. In the standard list all standards
defined in the assay are displayed. If the standards are always equal, enter the
respective value for each standard. Select the standard you want from the list and
then enter the value in the entry box above. If the standard values are variable, do
not enter any values here, but select the item Variable Std. Values. In this case you
are prompted to enter the standard values prior to each run.

Variable Std. The standard concentrations are variable. If you select

Values this item, you are prompted to enter the standard
concentrations prior to each run.
Variable Std. Check this item to use a multiplier for the entered
Multiplier standard concentrations.
Average Std. Select this item to use the average value of the specified
Reps. standard concentrations.

Stored Model This area are enabled if you select S t o r e d M o d e l in the D a t a Mo d e l menu.
FileName
Browse Click B r o w s e to select a file that includes the desired
evaluation curve (*.mod).
Use the Plate ID Allows the user to choose a plate (linked plate ID) with
as the file name the desired evaluation curve before a run.

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User-Defined Here you can enter a user-defined evaluation curve as formula. To enable this field
Model you have to select U s e r - D e f i n e d in the D a t a Mo d e l menu. Enter the curve
equation next to X =, and use for this the mathematical character offered in the
I n s e r t F u n c t i o n dialog box.
Input terms: This formula has to include 'Y ', 'S a m p l e' or 'S a m p l e . n' once (n =
individual value of cavity). Moreover, this edit box may contain: well labels, digits,
mathematical operators and brackets, as well as the functions offered via I n s e r t
Func tion. . . .

Insert Opens the I n s e r t F u n c t i o n d i a l o g box showing

Function... the available logical steps (see chapter 2.8 on page 2-108).

Notes Enter comments explaining the abbreviations.

Note The additional information entered here appears on the

printout of the result report. The input is automatically
entered in the menu above with an equal sign.
Expression Enter the expression (abbreviation) you want to explain.
This information is automatically entered in the menu
behind the equal sign.
List of notes Shows the defined notes which were entered in the two
edit boxes above.
Add Click on Add to insert an additional row with
explanation.
Remove Removes the highlighted row.
Clear Clears all notes in the N o t e s group box.

2.7.3.2 Model V.C.

You can subject the curve defined on the D a t a M o d e l tab to certain validation
criteria. To this end, you have to enter one or several control equations. An error
message appears if these are not fulfilled.
The r-squared value must be greater than 0.9: r2>0.9.
The slope value of a linear regression must be between 0.9 and 1.1: 0.9<=a(1)<=1.1.
The F-value of the data model must be significant at the 5% confidence level:
P(F)<0.05.
The M o d e l V . C . tab of the Q u a n t i t a t i v e S e t t i n g s dialog box is identical
with the V a l i d a t i o n C r i t e r i a dialog box (see chapter 2.7.1 on page 2-87).

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2.7.3.3 Dilution Tab

On this tab you define the dilution factor for each sample.

Figure 2-41: Q u a n t i t a t i v e S e t t i n g s dialog - D i l u t i o n s tab

T[x] Shows all samples selected in the test list below. In the
entry box you can edit the value (dilution factor) of the
sample selected from the menu. This entry is saved if
you select another test from the list.
Auto Fill... Opens the A u t o F i l l S e t t i n g s dialog box (see
below) and you can enter information for automatic
filling of the dilution table. Automatic filling starts with the
highlighted row. Enter a value for this dilution. For all
following cavities you can then define a multiple.

Auto Fill
Settings dialog
Box

Figure 2-42: Options for calculation the dilution factors

In this dialog you define automatic filling on the D i l u t i o n tab.

1. Select the dilution, starting with the first one you want to fill the table
automatically.
2. Enter the desired value for this dilution. Based on this value you can define in
the Auto Fill Settings dialog box a mathematical calculation (addition/
subtraction/division/multiplication) for all following dilutions.

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You can select the following mutually exclusive items:

Same as The following dilutions will have the same value as the
previous highlighted one.
Add to previous Add to each previous dilution the value defined in the
F a c t o r field.
Example: The highlighted value is 10, the factor 2, this
results in the series of numbers 10, 12,14, 16...
Subtract from Subtract from each of the previous dilutions the value
previous defined in the Fac t or field.
Example: The highlighted value is 100, the factor is 1,
this results in the series of numbers 100, 99,98, 97...
Multiply by Multiply each of the previous dilutions by the value
previous defined in the Fac t or field.
Example: The highlighted value is 10, the factor is 2, this
results in the series of numbers 10, 20, 40, 80...
Divide by Divide each of the previous dilutions by the value
previous defined in the Fac t or field.
Example: The highlighted value is 10, the factor is 2, this
results in the series of numbers 10, 5, 2.5, 1.25...
F ac t o r Enter the desired factor for the calculations. Default
value is 1.

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2.7.3.4 Graph Tab

On this tab you define the parameters for graphical presentation of the results.

Figure 2-43: Q u a n t i t a t i v e S e t t i n g s dialog - G r a p h tab

Enabled A graph is created only if this item has been selected in

the result printout and the graphics functions are
available on this tab.
S h o w a l l R e s u l t s Shows all results.
Show Error Bars Shows error bars.
Auto Automatic title.
Title Title of the graphical presentation.

X-Axis/Y-Axis Information on X or Y axis. If an item is checked in the Au to column, the respective

parameters are set automatically. Otherwise that value is used which has been
entered in the respective edit box.

Auto Automatic L a b e l , M i n i m u m , M a x i m u m or
Major Unit.
Label The label is taken from the assay definition or entered
manually.
Minimum Minimum value: automatic or manual setting.
Maximum Maximum value: automatic or manual setting.
Major Unit Automatic or manual setting.
Gridlines Show gridlines.
Logarithmic Logarithmic scale of the respective axis.
Scale

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2.7.3.5 International Units (I.U.) Tab

On this tab you define the formula for conversion of the concentration calculation in
I.U. (international units) into another unit.

Figure 2-44: Q u a n t i t a t i v e S e t t i n g s dialog - I . U . tab

X= Enter the formula.

Input terms: This formula has to include 'Y', 'Sa mp le '
or 'S a m p l e . n ' once (n = individual value of cavity).
Moreover, this edit box may contain: well labels, digits,
mathematical operators and brackets, as well as the
functions offered via I n s e r t F u n c t i o n . . . .
Result Units Designation of the result units.
Insert Opens the I n s e r t F u n c t i o n dialog and you can
Function... view and select the available logical operations (see
chapter 2.8 on page 2-108).

2.7.3.6 Validation Criteria Tab

Here you define validation criteria for single values. Enter one or several control
equations (e.g. S1>0.5). An error message appears if these are not fulfilled.
The V a l i d a t i o n C r i t e r i a tab of the Q u a n t i t a t i v e S e t t i n g s dialog is
identical with the V a l i d a t i o n C r i t e r i a dialog (see chapter 2.7.1 on page 2-87).

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Evaluation Definition

2.7.3.7 Annotation Tab

On this tab you define a text to be output instead of certain results. Enter the
conditions here.

Figure 2-45: Q u a n t i t a t i v e S e t t i n g s dialog - A n n o t a t i o n tab

Conditions
Condition In this field you enter the condition.
For example "Sample>2.5" means: "If the result > 2.5,
then use the character sequence in the R e s u l t
R e p l a c e m e n t field for result output instead of the
measured value."
The condition is automatically entered in the first row (or
if several rows exist, in the highlighted row) of the list of
conditions. Each row starts with "If". The entry you
make is automatically saved to this list and continues
the "If" condition. For example IF(>2.5).
You can make the entry via keyboard or by clicking the
I n s e r t F u n c t i o n . . . button. Click on New to define
a new condition.
Result Here you enter what should appear instead of the result
Replacement if the above given condition is fulfilled, e.g. "overflow".
The entries made here are automatically inserted in the
highlighted row of the list of conditions: e.g. IF
(Sample>2.5, Result:='overflow'. Process no further).
Result Here you can define a flag (e.g. a !) to annotate the
Annotation result which fulfils the above condition. The flag is
shown in the result reports.
The entries you make here are automatically inserted in
the highlighted row of the list of the conditions. e.g. IF
(Sample>2.5, Result:='overflow'. Flag='!').

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Evaluation Definition

Do not process If this item is checked, the results which do not fulfil the
result any criteria are not processed any further.
further
List of conditions Here the conditions are listed which are created via the
N e w C o n d i t i o n button.
Insert Function Opens the I n s e r t F u n c t i o n dialog box and you can
select a logical link for the description of your conditions
(see chapter 2.8 on page 2-108).
New Condition Click on this button to create a new condition in the list.
The new row starts with "IF..." You can define a condition
via keyboard or by clicking the I n s e r t F u n c t i o n . . .
button.
Delete Deletes the selected condition from the list of conditions.
Clear All Clears the entire list of conditions.
Move Up Moves the highlighted row in the list of conditions up one
row.
Move Down Moves the highlighted row in the list of conditions down
one row.
Undo Revokes the last action.
Redo Revokes the undo function.

Legends Here you can create a legend and provide explanations on the results and
abbreviations, etc.

Result Enter the term or the result you want to explain in the
legend. It is automatically entered in the first row of the
legend list or in case several legend rows exist in the
highlighted row.
Legend Enter a description. Separated by a tab mark, this text is
written in the same row as the result.
List of legends Result and legend, which were entered in the two edit
boxes above, are displayed separated by a tab stop.
New Legend Creates a new row for result and legend.
Delete Deletes the selected row from the legend list.
Clear All Clears the legend list.
Move Up Moves the highlighted row in the legend list up one row.
Move Down Moves the highlighted row in the legend list down one
row.

Reference You can type text or a formula (using the format function) into this field. The value of
Range this field will then be displayed in the results, stored in the sample results database
and transmitted to the LIMS. This field would normally be used to indicate what range
a normal result might be expected to lie within.

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2.7.3.8 Layout Tab

On this tab you define the layout for the data and result output.
It is identical with L a y o u t tab (see page 2-66) in the C o l o r i m e t e r S e t t i n g s
dialog box (see chapter 2.6.1 on page 2-64).

2.7.3.9 Retest Tab

Figure 2-46: Q u a n t i t a t i v e S e t t i n g s dialog - R e t e s t tab

Retest if Define condition under which a retest shall be executed.

N u m b e r t o r e t e s t This is the number of wells use when retesting the
sample, usually 1 or 2.
Insert Function Opens the I ns er t F u nc t i o n dialog box and you can
select a logical link for the description of your conditions
(see chapter 2.8 on page 2-108).
Retest with Define assay that shall be used for retest.
assay
Browse Click B r o w s e to select an assay for retest.
Result history This is to select what result history should be provided
when retesting the sample.
• No history:
The current result has no meaning.
• C u r r e n t r e s u l t.
For a retest that might need to know what original
result caused the retest.
• O r i g i n a l r e s u l t:
Initiate a retest using the original result (for cases
where the current result has no meaning).

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Report If checked then the software will report the current

intermediate result.
results If not checked then the software will not report the
current result (for cases where only the result of the
retest should be reported).
List of conditions Conditions, which were entered.
New Condition Creates a new row for condition.
Delete Deletes the selected row from the conditions list.
Clear All Clears the conditions list.
Move Up Moves the highlighted row in the conditions list up one
row.
Move Down Moves the highlighted row in the conditions list down
one row.

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2.7.4 Spreadsheet Parameters

Selecting S p r e a d s h e e t in the I n s e r t S t e p dialog opens the
S p r e a d s h e e t S e t t i n g s dialog.

Wrong results
It is necessary to validate assays to avoid wrong results.

2.7.4.1 Formulae Tab

Here you define the calculation formulae for each individual well (e.g. subtraction of
the OD of the control antigen from the OD-value of the antigen). The calculation
formulae are displayed on the plate layout in the respective fields.

Figure 2-47: S p r e a d s h e e t S e t t i n g s dialog - F o r m u l a e tab

A 1 ... H12 In front of this row you see the identification of the well
highlighted in the plate layout. Enter the desired
calculation formulae, (e.g. A1-A2, when the result of well
A2 is to be subtracted from the result of well A1). The
entries are automatically transferred to the highlighted
field of the plate matrix.
Insert Function Opens the I ns er t F u nc t i o n dialog box and you can
view and select the available logical links (see chapter 2.8
on page 2-108).
Plate layout Shows the entered formulae for calculation of the
reading results of the respective cavity.
Result Units Define the unit of calculated results.

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The function Va ria ble 1 cannot be used at present!

Handling:
• Use the mouse and press on the left mouse key to select a cell.
• Press on the Enter key to select the cell in the next row.

2.7.4.2 Other Tabs

All other tabs of the S p r e a d s h e e t S e t t i n g s dialog are identical with the
corresponding tabs of other dialogs:
• Layout Tab (see chapter 2.6.1.2 on page 2-66)
• Retest Tab (see chapter 2.7.3.9 on page 2-104)

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Entry of Logical Functions and Mathematical Signs

2.8 Entry of Logical Functions and

Mathematical Signs

For the assay definition you may enter formulae at various points. Enter the
mathematical signs (:, *, +, - ) via keyboard.
The logical functions are listed in the I n s e r t F u n c t i o n dialog, which appears
when you click the I n s e r t F u n c t i o n button. The logical functions must be
selected from this list. Otherwise, the program does not recognize the character
sequence as logical function.

Figure 2-48: I n s e r t F u n c t i o n dialog

A(n) Coefficient value.

This accesses the actual data model coefficient values.
If you wanted to use the slope of a linear regression in a
validation formula you would use A(1), if you wanted to
use the D parameter of a 4-parameter fit you would use
A(3).
abs Absolute value.
alog Uses the 10x anti-logarithm of the indicated value.
AND Logical AND link.
Chi2 Chi-squared value.
This is a statistical term which is calculated as the sum
of the squares of errors between the data points Y
values and their predicted Y values.
Column Current column number.
CV Calculates the coefficient of variation of the respective
well type or the plate, if no well types have been defined.
exp Uses the natural anti-logarithm of the indicated value.
F F-value.
This is a statistical term used in hypothesis testing. A
large F value indicates that the data model fits the data
well, a low value that it doesn't. See P(F) too.

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Entry of Logical Functions and Mathematical Signs

IF If the condition is true the "then" expression is

evaluated, otherwise the "else" expression.
Int Rounds the value down to the next integer value.
log Uses the 10x logarithm of the indicated value.
ln Uses the natural logarithm of the indicated value.
Max Indicates the maximum value of the respective well type
or the plate, if no well types have been defined.
Median Calculates the median of the respective well type or the
plate, if no well types have been defined.
Min Indicates the minimum value of the respective well type
or the plate, if no well types have been defined.
OR Logical OR link.
P(F) F-value probability.
This would be used in a hypothesis test as it tells you
the probability of achieving this F-value by chance
alone. So if you wanted to be 95% confident that you
had a good fit to the data points (i.e. only a 5%
probability that this is pure chance) you would write an
equation like "P(F)<=0.05".
P(T(n)) T-value probability. This is similar to above. If you
wanted to be 95% confident that your slope parameter
in a linear regression was modelling the data well you
would write an equation like "P(T(1))<=0.05". Note that
in all cases n is 0 based, so 0 is the first parameter, 1 the
second, etc.
R2 R2 value.
Result (expr) The result function replaces the O.D. value by the result
obtained by a processing step.
ROUND Rounded value.
Row Current row number.
Sample Current average well value.
Sample.n nth replicate of current well.
SE Calculates the standard error of the respective well type
or the plate, if no well types have been defined.
SD Calculates the standard deviation of the respective well
type or the plate, if no well types have been defined.
T(n) Coefficient t-value.
This is the student's t-value, another statistical term
used in hypothesis testing. Each coefficient of the data
model has its own t-value and this indicates how well it
is modelling the data in a similar manner to the F-value.
A low t-value indicates that the parameter isn't doing
much good (and could probably be removed); a high t-
value indicates that it is doing useful work in modelling
the data. See P(T(n)) too.

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Assay Programming
Entry of Logical Functions and Mathematical Signs

Variable1 If this function is selected, you may introduce a variable

(e.g. for a formula). The term "Variable 1" can be
overwritten by a test-specific term. If Variable 1 is
occupied, Variable 2 is created automatically; it can be
treated in the same manner. If Variable 2 is occupied,
Variable 3 is created, etc.
Valid (well type) Number of valid wells of the selected well type.
X(Y) Calculates the Y-value corresponding to the X-value.
Y Current replicate value.
This is used in user-defined data model formulae. As the
formula is evaluated for each well, there has to be some
way of getting the current OD value into the equation to
calculate a concentration and this is it. For example, if
you wanted to model a specific straight line, y=2x+3
then you would create a data model formula like "(Y-3)/
2".
Y(X) Calculates the X-value corresponding to the Y-value.
Y’(X) Gradient at X.

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 IFA Assay Programming (optional)
Introduction and Overview

3 IFA Assay Programming (optional)

3.1 Introduction and Overview

The Gemini COMBO instrument is an open system. It allows users to process pre-
defined assays but also to edit existing assays or to create their own assays.

Wrong results
New, modified or assumed assays must be validated to avoid wrong results.

Wrong results
If assays from a Gemini instrument will be used on a Gemini COMBO instrument,
they must be validated to avoid wrong results.

The instrument doesn’t generate any end result for slides. The slides will only be
prepared for further processing (e.g. evaluation under an external fluorescence
microscope) by the user.

Defining assays with the GEMINI COMBO instrument software is facilitated by

visual dialog boxes (no actual programming is needed) but because the system is
very flexible and allows users to define not only the processing steps but also the
result evaluation steps, defining assays remains a process that must be done with
adequate care and reference to the procedures described in this manual.
This introduction covers the basic concepts of IFA assay files (layout, structure,
protection). The second part is a step-by-step description of how to create completely
new assays.

Most of the processes of IFA and ELISA assays are similar, so in some chapters it
will only be referred to the corresponding chapter 2 of the ELISA description.

For assay programming, the use of an external mouse is recommended.

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IFA Assay Programming (optional)
Introduction and Overview

3.1.1 Defining a New IFA Assay

In the Gemini COMBO program you define a new assay by creating an assay file in
which all assay parameters are entered and saved. All assay files (*.asy) have the
same basic structure, consisting of some default assay steps and a list of freely
selectable assay steps which the user can arrange and define according to his
requirements.

Creating a new Proceed as follows:

IFA Assay File 1. Select the F i l e > N e w menu item.
2. Click on the A s s a y symbol.
3. In the S e l e c t A s s a y P r o t o c o l T y p e dialog, the items
C o l o r i m e t e r - E n d p o i n t , C o l o r i m e t e r - K i n e t i c (in
preparation) and I m m u n o f l u o r e s c e n c e are displayed.
4. Select the item I m m u n o f l u o r e s c e n c e to create a new IFA assay.

The display area (right) shows the slide layout and above some default settings. The
assay explorer tree in the left-hand side of this window shows the basic steps of an
assay. You can work with it in the same manner as you work with the Windows
Explorer: a folder including further information is identified by a plus sign (+). Click
on the plus sign to open the folder. An open folder is represented by a minus sign (-
). Click on the minus sign to close the folder.
The assay explorer tree, henceforth referred to as assay tree, includes the 4 basic
steps of an assay which cannot be deleted:

A s s ay H e ad e r Assay protocol header.

A s s ay L ay o ut Slide layout definition: layout of samples, standards and
controls on the slide.
Schedule break All assay steps from all assays of the worklist
programmed before the schedule break will be
performed in advance.
Report Settings Double-click on this step to open the respective
parameter window (see chapter 2.5.3 on page 2-44).
End of Protocol End of assay protocols.

Show Assay Click with the left mouse button on an assay folder to view the respective assay step
Step with the description of the already defined functions in the display area.

Edit Assay Step To edit an assay step, you always have to select the assay step to be edited.

Insert Assay To insert a new assay step, you always have to select the assay step in front of which
Step the new step is to be inserted.

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 IFA Assay Programming (optional)
Introduction and Overview

Context Menu The context menu for inserting new assay steps in a new assay can be selected via
for Inserting the menu item Edit on the menu bar, as well as by clicking the right mouse button on
Assay Steps the step before which the new step is to be inserted.

Undo Revokes the last action you have executed in the assay
tree.
Redo Revokes the last U n d o action again.
Cut Cuts out a highlighted assay step and saves it to the
clipboard.
Copy Copies a highlighted assay step to the clipboard.
Paste Inserts an assay step on the clipboard in front of the
highlighted assay step.
Edit To edit an assay step, you always have to select the
assay step to be edited.
Insert Step To insert a new assay step, you always have to select
the assay in front of which the new step is to be inserted.
Delete Deletes a step highlighted in the assay tree.
Select All Selects all assay steps.
Move Up Moves a highlighted assay step up one step.
Move Down Moves a highlighted assay down one step.
Execute Current Execute only the highlighted step of the selected assay
Step... (see notes below).
Execute Executes all remaining steps included the highlighted
Remaining step of the selected assay (see notes below).
Steps...

When you are performing the execute functions during a running worklist, the slide
will be scheduled into this running worklist!

General buttons
which apply on
OK Saves all entries and returns to the main menu.
most dialog
boxes Apply Saves the entries and the dialog box remains displayed.
Canc el Returns to the main menu without saving any entries.
Data that have already been saved by pushing Ap p l y
remain stored.
Help Calls on-line help.

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IFA Assay Programming (optional)
Introduction and Overview

3.1.2 Defining Assay Steps

Assay Header Double-click on this step to open the respective parameter window (see chapter 3.2 on
page 3-6).

Assay Layout Double-click on this step to open the respective parameter window (see chapter 3.3 on
page 3-12).

Scheduling Move this step to perform a schedule break (see chapter 3.4 on page 3-13).
Break

Definition of Click with the right mouse button on an assay step (exception A s s a y H e a d e r
possible Assay and A s s a y L a y o u t) to open the I n s e r t S t e p dialog box showing the
Process Steps available steps (see chapter 3.5 on page 3-15).

Report Settings Double-click on this step to open the respective parameter window (see chapter 3.6 on
page 3-20).

Saving the As soon as you have defined all steps, select the item F i l e > S a v e A s and save
Assay File the assay under a new name (extension *.asy).

3.1.3 Editing Existing Assays

See chapter 2.1.3 on page 2-9

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 IFA Assay Programming (optional)
Introduction and Overview

3.1.4 Basic Structure of Assay Files

All assay files (*.asy) have the same basic structure, consisting of some defaulted
assay steps (marked with a * in the table below) and a list of freely selectable assay
steps which can be arranged and defined according to the requirements of each test.

Assay Header *
The assay header includes general information such as: assay name, comments (if any),
password protection, written by, creation date, last edited, slide type used, maximum ambient
temperature as well as the possibility to enable the Include Sub-Assay feature and activate the
Dynamic Dilutions function.
Assay Layout *
Table representation of a slide showing the respective positions of the samples, standards and
controls for that assay.
Schedule break
All assay steps from all assays of the worklist programmed before the schedule break will be
performed in advance.
Assay steps (Processing steps)
Pipette Inserts a pipetting step (for samples, controls and
standards).
I FA W a sh Inserts a washing step.
Incubate Inserts an incubation step.
Dispense Inserts a dispense step (for reagents).
IFA dispense Inserts the IFA dispense step.
Report Settings *
Definition of the contents of the result printout, of the combined report and of the format and
contents of the result export file.
End of Protocol *

3.1.5 Password Protection for Assays

See chapter 2.1.5 on page 2-11

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IFA Assay Programming (optional)
Assay Protocol Header Information

3.2 Assay Protocol Header Information

Double-click on A s s a y H e a d e r in the assay tree to open the As sa y

P r o t o c o l H e a d e r dialog.

Description Name of assay.

Written by Name of the person/company who created the assay
protocol.
Combination The default combination group for all IFA assays is "0".
group
Comments Option to enter additional explanations.
Slide type Select a slide type.
Slide types Click this button to select the slide type you want to use
for this assay. Moreover, you can load the slide type
editor and create new slide types (see chapter 3.2.1 on
page 3-8).
Maximum Enter the maximum permissible room temperature. If
ambient temp. this temperature is exceeded, this will be indicated in the
result file.
Slide ID check Use this field to validate the slide ID.
The field can contain alphanumeric text and/or the
wildcard characters "*" or "?". A "*" is, therefore, always
OK. If the slide ID must start with an A then you would
use "A*". If the slide ID must have an A in the second
position then you would use "?A*".
Example: RUB*
• Slide ID ok:
• RUB20081105-1
• RUBAX_15
• Slide ID not ok:
• TOX20081102-2
• RUG20081105-1
Example: RUB_200?-*
• Slide ID ok:
• RUB_2008-1105-1
• RUB_2007-5
• Slide ID not ok:
• RUB_20081105-1
• RUB_200-5

Note: The minimum entry is a wildcard "*", otherwise

you get an error message.
Pressure Not available for the Gemini COMBO instrument.
Monitoring

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 IFA Assay Programming (optional)
Assay Protocol Header Information

Dynamic Dynamic dilutions are used to define different dilutions

dilutions for different samples (see chapter 3.5.1.1 on page 3-16).
Define Barcode Enables the dynamic barcode function for the assay
(see Ba rc od e button).
Barcode Allows to define a dynamic barcode format (see
chapter 2.2.2 on page 2-16).
Portfolio group The processing of assays can be limited with assay
portfolio groups. Only assays of the same assay
portfolio group could be used after the entry of an assay
portfolio group name (see also "Instructions for use
Manual", chapter "System Set-up").
Not allowed entries: space characters
I n c lu d e Su b - Defines the type of the assay:
Assay • Not marked: The current assay has no sub-assay.
• Marked: The current (primary) assay has a sub-
assay. The sub-assay will be created as a copy of the
primary assay. So the primary assay and the sub-
assay are identical. The assay layout and pipetting
steps of the sub-assay must then be changed. Note:
Incubation, IFA wash and IFA dispense steps cannot
be edited. The sub-assay will be stored in the same
*.asy file as the primary assay. The sub-assay is
marked with an asterisk.
See chapter 3.2.1.2 on page 3-11
Variables Shows the variables used in the assay which can be
deleted by clicking on the D e l e t e button.
If they are used for the assay, they must not be
deleted.
Labels Shows the labels used in the assay which can be
deleted by clicking on the D e l e t e button. Input of the
label or variable is not possible here, but is automatically
carried out by the system after they have been defined
in later process steps (see chapter 3.5.1 on page 3-16).
If they are used for the assay, they must not be
deleted.

Password Option to enter a password. This rules out that the assay can not be modified by
anyone who does not know the password. However, no password is required to run
the assay.

Password Enter the password

Retype Repeat the same password.
password

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IFA Assay Programming (optional)
Assay Protocol Header Information

3.2.1 Creating Slide Types

Click on the S l i d e T y p e button in the As s a y P r o t o c o l H e a d e r dialog to
open the S l i d e T y p e E d i t o r dialog, showing the slide types available on the
system and allowing you to generate new ones. The coordinates of the slide type will
be saved to a *.rac file in the program directory. The S l i d e T y p e E d i t o r dialog
allows you to create new slide types from existing slide (*.rac) files available on the
system. It does not allow you to create new (*.rac) files. If you need to create new
(*.rac) files, please contact your service engineer. New slide *.rac files must be
created using the Teacher software. In the Teacher software the coordinates of the
individual slides are taught.

List of slide types Selection box listing the slide types pre-defined for the
system.
Slide overview Shows the selected slide type as overview. Click on a
well to select a position.
Slide name The name of slide type highlighted in the menu is
displayed. Click on Ad d to define a new slide type and
enter a new name. This will create a new plate type
which has to be combined with a *.rac file, i.e. you have
to choose a *.rac file in the S l i d e f i l e drop-down
menu.
Slide file Drop-down menu showing the available *.rac files.
These files contain the slide coordinates and are
created using the teacher software.
Colour Drop-down menu to select the color of the slide. The
slide will be shown with this color in the user software.
Note: Use different colors for slides with similar layout.
User will be recognized that slides are different.
Position Selection of the slide wells. If you select a position, the
dialog shows the corresponding shape, offsets and
sizes.
Shape Select the shape of the well (circle or rectangle) in mm.
O f f s e t X /O f f s e t Y Position of the selected well on the slide in mm (see
figure 3-1: on page 3-9).
• X = 0: right side of the slide picture (right side of the
real slide)
• Y = 0: upper side of the slide picture (rear side of the
real slide)
S i z e X /S i z e Y Size of the selected well (see figure 3-1: on page 3-9).
Add Click this button to create a new slide type (see below).
The generated slide type is entered in the menu to the
left and it has to be combined with an *.rac file.
Delete Deletes the slide type highlighted in the selection box.
OK Closes the S l i d e T y p e E d i t o r dialog. Changes
are saved. The program returns to the A s s ay
P r o t o c o l H e a d e r dialog.

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 IFA Assay Programming (optional)
Assay Protocol Header Information

Figure 3-1: Explanation of the slide well positions and sizes

Wrong pipetting results

Changes of the slide well positions and sizes must be validated to avoid wrong
pipetting results.

3.2.1.1 Adding new Slide Types

Proceed as follows:
1. Click on Ad d .
Enter the desired slide type name into the N a m e box.
2. Enter the desired number of wells into the P o s i t i o n s box.
3. Click on the OK button.
4. Enter in the A d d p o s i t i o n dialog the O f f s e t X, the O f f s e t Y, the
S i z e X , and the Siz e Y (see figure 3-1: on page 3-9).
5. Click on the OK button.
6. Repeat the add position steps for all positions.
7. After the last position the previously defined slide type is displayed in the list
of available slide types.
8. Click on O K to accept the generated slide type and to return to the A s s a y
P r o t o c o l H e a d e r dialog.

The user is asked to confirm changes in the S l i d e E d i t o r with O K before

changes are saved.

Wrong pipetting results

New slide types must be validated to avoid wrong pipetting results.

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IFA Assay Programming (optional)
Assay Protocol Header Information

Maximum of 12 wells
A maximum of 12 wells is specified but more wells can be added on own risk. Only
validated assays can be run on the Gemini Combo.

Assays with sweep function

For assays using the sweep function in the IFA wash step Size X and Size Y may be
added with a smaller diameter than measured to avoid that the IFA needle reaches
the hydrophobic surface outside the well.

Correct parameters
The software uses Size X and Size Y parameters for calculating the dimensions of
the slide well which will be used for the In-Well Multishot feature. Make sure that
these parameters are correct.

Slide identification
To avoid confusion it will be useful to choose similar slide names and rac file names.

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 IFA Assay Programming (optional)
Assay Protocol Header Information

3.2.1.2 Primary- and Sub-Assays

Sub-assays can be used to reduce the number of controls on slides from the same
batch. This allows testing more samples with the same number of slides. For this
purpose, an IFA assay is divided into two parts:
• Primary-assay: Assay with controls and samples.
• Sub-assay: Assay only for samples.

A sub-assay contains all steps from the primary assay, but P i p e t t e and
Di s p e n s e steps could be customized.

How to create a primary- and a sub-assay?

1. Create a new assay with all necessary steps.
2. Check the assay.
3. Open the primary assay and mark the I n c l u d e Su b - A s s a y checkbox.
4. Select the menu item View | Sub- as say to show the sub-assay. The
system writes a ’*’-character before the assay name in the assay tree.
5. Change the P i p e t t e and D i s p e n s e steps and the assay layout. Note:
Incubation, IFA wash and IFA dispense steps cannot be edited.
6. Check both assay parts.

The sub-assay must not be created after finalization of the primary assay.

Change primary-assay and lost sub-assay

If you are using the sub-assay function and you will change the primary-assay, you
must unmark the I n c l u d e S u b - A s s a y checkbox. But if you do that, the sub-
assay and all settings will be lost.

Same steps in primary-assay and sub-assay

Primary- and sub-assay should have the same steps. Only differences between
controls should be present.

Verify assay
The V e r i f y A s s a y function checks either the primary assay or the sub-assay
depending on the currently selected view. It must be assured that the basic steps are
equal especially after changes in primary assay or sub-assay are done. Validation of
assay and correct databases are required.

Use of primary- and sub-assay

The user can decide whether to:
• use the primary-assay for all slides of a worklist (Choice A l w a y s )
• use the primary-assay only for the first slide. For all other slides the system
uses the sub-assay (Choice O n c e )
• use only the sub-assay for all slides of a worklist (Choice N e v e r )

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IFA Assay Programming (optional)
Assay Layout Definition

3.3 Assay Layout Definition

See chapter 2.3 on page 2-18, replace plate with slide.

Replicates, dynamic dilutions and sub-assays

Do not use replications together with the dynamic dilutions and sub-assays functions!

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 IFA Assay Programming (optional)
Scheduling Break

3.4 Scheduling Break

All assay steps from all assays of the worklist programmed before the schedule
break will be performed in advance.
The Sc h e d u li n g b r e a k step can be changed by the Mo v e u p and M o v e
d o w n functions in the Context Menu for Inserting Assay Steps.
Example:
The assay has at first the pipette step, followed by the schedule break and a second
pipette step.

Figure 3-2: Assay with scheduling break

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IFA Assay Programming (optional)
Scheduling Break

The scheduling shows, that at first the sample pipetting of all slides will be performed;
after this step, the slides are scheduled according the remaining assay steps.

Figure 3-3: Worklist with scheduling break

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 IFA Assay Programming (optional)
Definition of Assay Steps

3.5 Definition of Assay Steps

An assay is programmed by adding individual processing steps.

Click with the right mouse button on an entry (after the step A s s a y L a y o u t) in
the assay tree and then select I n s e r t S t e p in the menu window. The I n s e r t
St ep dialog box is displayed, showing the assay steps you can select.

Pipette Inserts a pipetting step to aspirate/dispense samples

and controls (see chapter 3.5.1 on page 3-16).
IFA Wash Inserts a wash step (see chapter 3.5.2 on page 3-17).
Incubate Inserts an incubation step (see chapter 3.5.3 on page 3-
19).
Dispense Inserts a dispense step (see chapter 3.5.4 on page 3-19).
IFA dispense Inserts the IFA dispense step (see chapter 3.5.5 on page 3-
19).

After selection of a step the respective dialog box is displayed for parameter entry.
Once you have entered your parameters and saved your entries, the new step is
inserted in the assay tree.

Order of Assay You can arrange the individual steps in any order. The order is defined during new
Steps definition of a step by clicking with the right mouse button on the folder before the
one you want to place the new step.
But when defining your steps, you can freely add them in any order to start with
(some are easier to define than others) and then rearrange them in the correct order
of the assay with the M o v e U p / M o v e D o w n items of the E d i t menu (or of
the context menu).

Editing Assay Double-click on the respective symbol in the assay tree to open the respective
Steps parameter window.

Replicate steps If your assay includes steps that are repeated identically or almost identically (this is
often the case for I F A W as h steps or I n c u b a t i o n steps), you can speed up
the definition process by using the C o p y / P a s t e function of the E d i t menu (or
of the context menu). Edit the parameters if necessary.

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IFA Assay Programming (optional)
Definition of Assay Steps

3.5.1 Pipetting Steps

See chapter 2.5.1 on page 2-28, replace plate by slide.

Additional parameter on the Dis p en se dialog (see chapter 2.5.1.3 on page 2-34):

Incompatible functions
When using the I n - W e l l M u l t i s h o t s feature the I n l i q u i d d i s p e n s e
function must not be activated.The software uses size X and size Y parameters
added in the Sl i d e E d i t o r for calculating the dimensions of the slide well. Make
sure that these parameters are correct.

In-Well The number of I n - W e l l M u l t i s h o t s

Multishots defines how many dispense steps are
executed within one well. The volume for each
in-well dispensing is calculated by the
software. The software distributes evenly the
overall volume to all dispense steps.

3.5.1.1 Dynamic Dilutions

IFA assays offer the possibility of the so-called dynamic dilutions. This means that a
sample can be pipetted in different dilutions into an IFA slide well. After selection of
the IFA assay, the user decides which dilutions of the individual sample should be
applied. For each selected dilution for a sample a new well is used on the slide (e.g.
1 sample * 2 dilutions = 2 assigned wells).

1. Activate the D y n a m i c d i l u t i o n s function in the Ass ay Prot oc ol

H e a d e r dialog (see chapter 3.2 on page 3-6).
2. Add a dilution and a transfer step to the pipetting steps:
• Dilution step: Aspirate the sample and reagent liquid. Dispense the
liquid into a dilution plate with an expressive and unique L a b e l . The
L a b e l will be shown later in the S e l e c t D i l u t i o n s dialog.
• Transfer step: Aspirate the liquid from the dilution plate (note the
correct L a b e l ). Dispense the liquid onto an IFA slide.
3. Check if all steps programmed in the D il u t i o n step are programmed in the
Tr ansf er step.

Insufficient liquid
If the liquid volume of a dilution is not sufficient, it can happen that the liquid volume
for the following dilutions and the transfer step is insufficient.
• Take care that sufficient liquid volume for serial dilution and transfer step is
inside the dilution well.

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 IFA Assay Programming (optional)
Definition of Assay Steps

3.5.2 IFA Wash Steps

Here you define the parameters used when slides are washed with the IFA pipettor
needle. The pipettor aspirates and dispenses at the same time.
The W a s h dialog lets you define different parameters for the wash cycle.
Select the IFA Wash item in the I n s e r t S t e p dialog (see chapter 3.5 on page 3-
15). The W a s h dialog appears.

Sweep The sweep parameters are used for washing wells on a slide.
parameters
Number of Describes how often the pipettor needle moves within a
s we e p s well. The track of these moves depends on size of well.
Z Offset The Z offset parameter describes the distance above
Zmax. Zmax is the lowest position of the pipettor needle
in the slide area. Zmax is taught using the Teacher
software.
Sweep speed Sets the X-/Y-move speed of the pipettor during the
sweeps. The speed parameter is in percentage of
maximum speed of the pipettor.
Delay The delay parameter describes the time between start of
aspiration pump and start of dispense pump.
Cycles Defines how often all used wells of one slide shall be
washed. A new cycle begins if all used wells of a slide
were washed.
Final aspirate The marked checkbox F i n a l a s p i r a t e moves the
needle to the height of Z D o w n O f f s e t . During this
movement only the aspirate pump is active. This feature
allows optimal slide washing and to minimize the liquid
remaining on the slide well for the last wash cycle.
Z Down Offset The Z D o w n O f f s e t parameter defines the offset
above Zmax. The aspirate pump switches off, if
Z D o wn O f f s e t is reached.

Dispense pump
parameters
Speed The dispense pump parameter speed value is in
percentage of maximum dispense pump speed.

Wash Buffer To select the wash buffer, click the arrow button to open the drop-down list. If the
desired buffer is not included in the list you may define it by clicking the B u f f e r s
button (see chapter 2.5.11.1 on page 2-59).

Buffers If the desired buffer is not available in the drop-down list,

you may define or load another wash buffer by clicking
this button to open the S e l e c t R e a g e n t s dialog
with the wash buffers available on the system. Select
the desired wash buffer to be used with the respective
assay (see chapter 2.5.11.1 on page 2-59).

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IFA Assay Programming (optional)
Definition of Assay Steps

Wash needle Parameters to wash the pipettor needle itself.

Duration The duration time defines the complete pipettor needle

wash time. The pipettor moves to the wash station and
starts priming and aspirating as long as it is defined in
duration time.
Pipettor needle • A f t e r e a c h w e l l: Washes the pipettor needle
washing after each well wash step.
• A f t e r e a c h c y c l e: Washes the pipettor needle
after each cycle.
• A f t e r c o m p l e t e s l i d e : Washes the pipettor
needle after the complete wash step.
• N e v e r: Do not wash the pipettor needle.
Wash before Washes the pipettor needle before the first well will be
first well washed.

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 IFA Assay Programming (optional)
Definition of Assay Steps

3.5.3 Incubation Steps

Slides can only incubate at room temperature.

See chapter 2.5.3 on page 2-44

3.5.4 Dispense Steps

See chapter 2.5.4 on page 2-46, replace plate with slide.

3.5.5 IFA Dispense Steps

In the last IFA assay step the slide wells shall be covered with fluid (e.g. IFA wash
buffer) which can be selected in this step.
Select the I F A D i s p e n s e item in the I n s e r t S t e p dialog (see chapter 3.5 on
page 3-15). The C o v e r dialog appears.

Cover Height for fluid dispensing, to avoid the aspiration of liquid on the slide.
parameter
Z Start Start height for dispensing.
Z Stop Stop height for dispensing.

Wash Buffer To select the wash buffer, click the arrow button to open the drop-down list. If the
desired buffer is not included in the list you may define it by clicking the B u f f e r s
button (see chapter 2.5.11.1 on page 2-59).

Buffers If the desired buffer is not available in the drop-down list,

you may define or load another wash buffer by clicking
this button to open the S e l e c t R e a g e n t s dialog
with the wash buffers available on the system. Select
the desired wash buffer to be used with the respective
assay (see chapter 2.5.11.1 on page 2-59).

Dispense pump
parameters
Speed The dispense pump parameter speed value is in
percentage of maximum dispense pump speed.

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IFA Assay Programming (optional)
Report Settings

3.6 Report Settings

The system doesn’t generate any end result for slides. The slides will only be
prepared for further processing (e.g. evaluation under an external fluorescence
microscope) by the user.

See chapter 2.6.3 on page 2-73

Additional parameter in the lists of the R e p o r t S t r u c t u r e area on the R e p o r t

tab (see chapter 2.6.3.1 on page 2-73):

List entry • Layout

Shows the slide layout in the test report.

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 Index

4 Index

A Evaluation definition ..............................2-86

Evaluation steps .....................................2-63
Assay layout definition ..........................2-18 Export
Assay layout definition (IFA) .................3-12 ASTM E 1394 .........................................2-84
Assay layout dialog ...............................2-18 Text file ...................................................2-82
Assay Programming ................................2-1
Assay Programming (IFA) ......................3-1
Assay protocol header information ......2-12
F
Assay protocol header information (IFA) 3- Functions ..............................................2-108
6
Assay steps ..............................................2-7
I
Assay steps (IFA) ............................3-4, 3-15
Assay steps before read .......................2-26 Incubate verification steps ....................2-57
ASTM E 1394 export .............................2-84 Incubation steps .....................................2-44
Incubation steps (IFA) ...........................3-19
B Introduction ...............................................1-1

Background read steps .........................2-53

L
Background subtraction ........................2-70
Layout definition .....................................2-18
C Layout definition (IFA) ...........................3-12
Logical functions ..................................2-108
Conditional delay steps .........................2-54
Create assay layout ...............................2-20
M
Creating plate types ..............................2-15
Creating slide types .................................3-8 Mathematical signs ..............................2-108
Multi-preparation assays .........................2-5
D
N
Defining a new assay ..............................2-2
Defining a new assay (IFA) ....................3-2 New assay ................................................2-2
Defining assay steps ...............................2-7 New assay (IFA) .......................................3-2
Defining assay steps (IFA) ......................3-4 Notes .........................................................1-1
Dispense steps .......................................2-46
Dispense steps (IFA) .............................3-19
O
Dispense steps (IFA), Cover (IFA) .......3-19
Dynamic barcodes .................................2-16 Overview about assay programming .....2-1
Dynamic dilutions ...................................3-16 Overview about assay programming (IFA)
3-1
E
Edit assays ...............................................2-9

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Index

P V
Password protection ............................. 2-11 Verify dispense steps ............................ 2-50
Pipetting steps ....................................... 2-28
Edit operation ......................................... 2-31
W
• Aspirate parameters .......................... 2-32
• Dispense parameters ........................ 2-34 Warning symbols ..................................... 1-2
• Eliminate assay drift .......................... 2-36 Warnings ................................................... 1-1
Pipetting steps (IFA) .............................. 3-16 Wash steps ............................................. 2-38
Plate types .............................................. 2-15 Wash steps (IFA) ................................... 3-17
Primary-assay ........................................ 3-11

Q
Qualitative evaluation ........................... 2-89
Qualitative settings ................................ 2-89

R
Read definition ....................................... 2-63
Reader settings ..................................... 2-64
Reagent database ................................. 2-59
Create a reagent .................................... 2-60
Edit a reagent ......................................... 2-60
Reagents selection ................................. 2-59
Report settings ....................................... 2-73
Report settings (IFA) ............................. 3-20

S
Safety instructions ................................... 1-4
Scheduling break .......................... 2-24, 3-13
Shake steps ........................................... 2-56
Slide types ................................................ 3-8
Special types ............................................ 1-3
Spreadsheet parameters .................... 2-106
Structure of assay files ......................... 2-10
Structure of assay files (IFA) .................. 3-5
Sub-assays ............................................ 3-11
Symbols
Warning .................................................... 1-2

T
Temperature inside the instrument ...... 2-44
Text file export ........................................ 2-82
Typographical conventions .................... 1-1

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