BIOINFORMATICS

MICROBIOLOGY
Report

Submitted
in
BIOTECHNOLOGY

by

Adnan Ahmad (Roll No.2301330540003)

Under the Supervision of

Er. Neeraj Agarwal & Dr. Sonia Verma

Dr. Ruchira Bajpai

Affiliation: AKTU
Objective
:-

Perform a BLAST search on a MDM2 protein sequence.

Demonstration and hands on
Training
Tasks :-
for Digital Microscope
Demonstrating and providing hands-on training for a
digital microscope involves several key steps to
ensure● Use
that users from
a sequence understand
a nucleotide how to database
or protein operate the
equipment properly and maximize its capabilities for
(GenBank, EMBL).
various tasks.
● Conduct a basic and advanced BLAST search (e.g., PHI-BLAST,
PSI-BLAST).
.Preparation

.Introduction to Digital Microscopes

● Analyse alignment scores, E-values, and conserved regions.
.Demonstrating the Components of the Digital Microscope
● Identify homologues, orthologues, and paralogues.
.Basic Operating Procedures

.Hands-On Practice
● Discuss the scoring matrices (e.g., PAM/BLOSUM) and gap
. Best Practices
penaltiesand Safety Considerations
applied.
 ACKNOWLEDGEMENTS

I would like to express my gratitude towards Dr. Ruchira Bajpai for their guidance and
constant supervision as well as for providing necessary information regarding the report & also for
their support in completing the work.

My thanks and appreciations to respected HOD, Mrs. RASHMI MISHRA for their motivation and
support throughout.
1. Introduction and Overview
Objective: Briefly introduce the purpose of the digital
microscope, its components, and its practical applications.
Key Points to Cover:
What is a digital microscope and how it differs from optical
microscopes.
Applications in fields like biology, material science,
electronics, forensics, etc.
Importance of digital imaging in modern microscopy.
2. Familiarize with the Components
Objective: Make the participants familiar with the different
parts of the microscope.
Key Components to Discuss:
Eyepiece: If the microscope has an eyepiece, describe what it
does.
Objective Lenses: Describe the different magnifications and
how they work.
Camera/Camera Interface: Describe how digital imagery
works. Describe the camera's resolution and how it connects
to a computer.
LED Light Source: Display control of light intensity to be
achieved for clarity.
Focus Mechanism: Illustrate coarse and fine adjustments.
Stage: Describe how to place the sample or slide on the
stage.
Software: Describe the purpose of any associated software
with image capture and analysis.
3. Digital Microscope Setup
Objective: Demonstrate how to configure the digital
microscope appropriately prior to use.
Steps:
Turn on the microscope and make sure all components are
working.
Tilt and adjust the camera height to view the sample as
clearly as possible
Set the light source to position the sample for proper
illumination
Verify the camera is connected to a computer or monitor.
Adjust the software settings if necessary (e.g., resolution,
frame rate).
4. Sample Preparation
Goal: Train users on how to prepare samples for observation
on the microscope.
Steps:
Mount or place the sample on the microscope stage
correctly.
Describe the use of slides, coverslips, or specimen holders.
Emphasize any sample preparation methods (e.g., staining for
biological specimens).
5. Basic Operation
Goal: Show how to operate the microscope for basic
observation.
Steps:
Change the magnification: Focus the sample with the coarse
focus knob and use the fine focus knob to center it.
Change magnification with the objective lens: Switch in and
out between the different lenses and show what effect this
has on the overall magnification of the sample
Lighting Changes: Adjust intensity and position the light to
create an optimal view
Camera Controls: Take pictures of the sample with the digital
camera.
Software Adjustments: Provide information on the way to
make changes in software, such as changing brightness,
contrast, or color balance settings within the microscope's
software.
6. Practical Exercises
Purpose: Give individuals time to operate the microscope
independently
Actions:
Distribute various sample types, either biological, material-
based, or others.
Provide access to prepare the samples for the microscope
and various ways of using a focus or the magnification
options.
Grant sufficient time for exploring the capturing software and
processing the data.
Walk the class through solving for common problems, such as
out-of-focus images or incorrect lighting.
7. Software to Analyze Images
Goal: Practice using the supporting software for analysis and
recording.
Tasks:
Image Acquisition: Demonstrate the acquisition and saving of
clear, high-resolution images of specimens.
Measurement and Analysis: Depending on the capabilities of
the software, demonstrate its ability to measure, such as the
distance, area, or details of an object.
Annotation Tools: Demonstrate annotation and labeling tools
within the software.
Export Data: Explain how to save or export images and data
for reports or further analysis.
8. Advanced Techniques
Goal: Explore additional advanced features, if the microscope
or software permits.
Process:
Image Stacking: Demonstrate how to use software on a
microscope platform to stack images, so to speak, in order to
combine multiple images at different focal depths to create a
more detailed image.
3D Imaging: If the equipment permits 3D imaging,
demonstrate the process for creating 3D reconstructions of
samples.
Comparative Analysis: Demonstrate how to compare several
images or how change can occur in a matter of time by
showing time-lapse features.
9. Troubleshooting
Goal: Focus on common issues and questions which are likely
to surface during the session.
Steps:
Image Quality Problems: Explore issues like bad resolution or
even the image blur. How one will solve those, for instance
adjusting the focus and lighting along with settings.
Software Issues: Offer solutions like problems with camera
and saving an image.
Calibration: If it is necessary, describe how to calibrate the
microscope so measurements are accurate.
Tips for Successful Hands-On Training:
Make It Interactive: Invite questions and make sure the
participants are hands-on.
Adjust the Pace: Vary the pace according to the comfort of
the participants and their experience with microscopes.
Printed Resources: Provide handouts or digital guides for use
after the training session.
Check Progress: Roam around the room to offer one-on-one
support if needed while practicing hands-on.

A Culture media of E.Coli.

Introduction to Digital Microscopes and Their
Utility & Advantages
A digital microscope, in a simplified term, represents a
modern adaptation of the optical version, meant for
the incorporation of advanced imaging systems with
digital data processing. Differing significantly from
traditional, conventional microscopes, which can only
be inspected through an eyepiece and do not typically
provide real-time microscopic vision through a screen,
a digital microscope captures sharp images at close
distances and views them on its screen. These
microscopes will often include an integrated digital
camera, a high-performance optical system, and
custom software for the capture, analysis, and
processing of images. They are being used in
biotechnology, material science, electronic, forensic
work, and other industrial quality-control applications.

Practical Applications of Digital Microscopes

 The flexibility, ease of use, and the broad support
of applications constitute the utility of digital
microscopes.

 Research and Education: Digital microscopes are

powerful tools for scientific research and
educational purposes. They enable students,
 researchers, and educators to explore and
document specimens with unprecedented clarity.
Recording, saving, and sharing images in real time
enhances learning and collaboration in classrooms
and laboratories.

 Medical and Biological Applications: In biology and

healthcare, digital microscopes are used in the
examination of specimens such as cells, tissues,
and microorganisms. They assist in medical
diagnostics, drug testing, and genetic research.
Some data acquisition software can also be
integrated for more advanced studies, like
quantifying cell morphology or counting bacterial
colonies.

 Material Science and Engineering: Digital

microscopes are widely used in analyzing materials
at the microscopic scale. They are employed in
electronics, metallurgy, and manufacturing to
inspect components, measure surface features,
and detect defects. Being able to view the surface
structure and internal features of materials makes
them invaluable for quality control.
  Forensics: The digital microscopes enable the
examination of trace evidence, including fibers,
hair, and gunshot residues, for analysis by forensic
experts to determine their origin. Digital
microscopes also help enhance forensic
investigations by providing high-resolution images
of traces.

 The primary application of digital microscopes can

be seen in the inspection and quality control
operations within precision manufacturing
industries, such as electronics, automobiles, and
aeronautics. These organizations use digital
microscopes to visually inspect small items like
circuit boards, microchips, and machine parts
before shipping products with even the tiniest
flaws.

Advantages of Digital Microscopes

 Ease of Use: Unlike the traditional microscopes,
digital microscopes do not strain users' eyes by
looking through eyepieces. The large screen
interface is much easier to use and view, focus, and
 manipulate samples compared to traditional
microscopes. This is especially beneficial for new
users of microscopy or people with visual
impairments.

 High-Resolution Imaging: Digital microscopes often

feature high-quality cameras with advanced
imaging sensors, enabling users to capture
extremely detailed images at various magnification
levels. This is especially useful for applications
requiring precision, such as in medical diagnostics
or material analysis.

 Digital image capture: Through its built-in camera

and digital interface, it can be used to take
snapshots or videos of the specimens in practice.
This is helpful for documenting research, making
photographic or video records, and sharing the
findings with other people. It also makes it easy for
the creation of presentation materials, or
publication-ready images.

 Enhanced Image Processing and Analysis: Many

digital microscopes come with accompanying
 software that enables real-time image
enhancements, measurements, and detailed
analysis. Users can adjust brightness, contrast, and
focus, and apply filters for clearer visuals.
Advanced tools may include features such as
image stacking, 3D imaging, and automatic
measurements, which are particularly beneficial
for research and industrial applications.

 It can allow more than one user to view the same

image at the same time by being connected to a
computer, projector, or other displays. Therefore,
digital microscopes are perfect for group work;
during the setup, researchers, students, or teams
can discuss matters while viewing the same
specimen, creating an interactive and more
efficient work environment.

 Data Storage and Retrieval: Unlike traditional

microscopes, which rely on physical notes and
sketches to keep all that data, digital microscopes
allow easy storage of data. Images, videos, and
even analysis results can be saved and organized
digitally for later reference; hence, one can easily
 track the changes, compare results, or retrieve
certain data for reports and publications.

 Portability and Flexibility: Digital microscopes often

come in compact and lightweight variants. This
makes them convenient for transportation in the
field or to any location for inspection. There are
even models that are USB-powered, easily
connectible to laptops and tablets, making them
flexible for use in a variety of work environments.

 Cost Efficiency: Even though the cost of a digital

microscope may be higher at first, it may end up
saving in the long term because complex
equipment is minimized, and processes become
more efficient. It saves on time as one can directly
capture and analyze images instead of manual
documentation.