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Angio Genesis Quant If Ication

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7 views28 pages

Angio Genesis Quant If Ication

Uploaded by

dadhichakshay181
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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Developmental Biology

(M.Sc. Practical)

Prof. Alok C. Bharti


Molecular Oncology Laboratory
Department of Zoology, University of Delhi
Delhi-110007
Analysis of angiogenesis in chick CAM

A. Qualitative Assessment- Photographs

B. Quantitative Assessment- Image Processing


using ImageJ software
Parameters to be included:
• Number of nodes
• Number of meshes
• Total branch length
Image J software
• ImageJ is public domain software for processing
and analyzing scientific images.

• It is written in Java, which allows it to run on many


different platforms such as Linux, Mac OS X and
Windows, in both 32-bit and 64-bit modes.

• We can use ImageJ to display, annotate, edit,


calibrate, measure, analyze, process, print, and
save image data.
Part I
Downloading and Installing
the ImageJ software
Part 1: Downloading and Installing the
ImageJ software
Step 1: Open your browser and type “Image J software
download” in your search bar.
Part 1: Downloading and Installing the
ImageJ software
Step 2: In the search results obtained, open the website
imagej.nih.gov > download
Part 1: Downloading and Installing the
ImageJ software
Step 4: Now download the software according to
specification of your system using given links

For Macbook

For windows with


64-bit operating
system
Part 1: Downloading and Installing the
ImageJ software
Step 4: Now extract the files from zipped folder and install
the software
Part 1: Downloading and Installing the
ImageJ software
Step 5: ImageJ software is installed and ready for use.
Part II
Downloading the
Angiogenesis Plugin
Part 2: Downloading the Angiogenesis
Plugin
Step 1: Open the link https://imagej.net/software/fiji/ for
downloading Fiji software.
Part 2: Downloading the Angiogenesis
Plugin
Step 2: Go to downloads and extract the files from
downloaded zipped folder for future use.
Part 2: Downloading the Angiogenesis
Plugin
Step 3: Open your browser and type “angiogenesis analyzer
for Imagej plugin download” and open the website
BioImage Informatics Index (biii.eu)
Part 2: Downloading the Angiogenesis
Plugin
Step 4: Click on the “ source code link” and the code will
appear
Part 2: Downloading the Angiogenesis
Plugin
Step 5: Save the code in the “txt file” by clicking on save as
Part 2: Downloading the Angiogenesis
Plugin
Step 6: Once the source code file is saved, open your
ImageJ application, then go to ImageJ > Plugins > Macros >
Install
Part 2: Downloading the Angiogenesis
Plugin
Step 7: After clicking on install, open the downloaded
source code file.
Part 2: Downloading the Angiogenesis
Plugin
Step 8: After clicking on install, open the downloaded
source code file, all angiogenesis related functions will
appear.
Part III
Angiogenesis Quantification
using ImageJ
Part 3: Angiogenesis Quantification using
ImageJ
Step 1: Go to ImageJ > File > Open and select your picture
to be quantified
Part 3: Angiogenesis Quantification using
ImageJ
Step 2: Go to ImageJ > Image > Type > 8-bit
Part 3: Angiogenesis Quantification using
ImageJ
Step 3: Go to ImageJ > Image > Adjust > Threshold
Part 3: Angiogenesis Quantification using
ImageJ
Step 3: In the threshold dialogue box, check dark back
ground option and colour B&W and then click on apply.
Part 3: Angiogenesis Quantification using
ImageJ
Step 4: Now again go to ImageJ > Process > Binary >
Skeletonize.
Part 3: Angiogenesis Quantification using
ImageJ
Step 5: Once the picture is skeletonized, go to
Angiogenesis Plugin > Analyze Binary Tree
Part 3: Angiogenesis Quantification using
ImageJ
Once the analysis is complete, you will get number of
nodes, meshes and total branch length in the Stat Results
Table. Copy this number and make graph in excel
Part 3: Angiogenesis Quantification using
ImageJ
Step 6: Again go to Angiogenesis Plugin > Save current
analysis
Suggested Paper

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