BY Bhimanathini Venkatsai Sai Kumar Maddula PROJECT#3(b) Astrocyte Analysis.
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Transcript of BY Bhimanathini Venkatsai Sai Kumar Maddula PROJECT#3(b) Astrocyte Analysis.
![Page 1: BY Bhimanathini Venkatsai Sai Kumar Maddula PROJECT#3(b) Astrocyte Analysis.](https://reader036.fdocuments.in/reader036/viewer/2022062519/5697bfae1a28abf838c9c65d/html5/thumbnails/1.jpg)
BY Bhimanathini VenkatsaiSai Kumar Maddula
PROJECT#3(b)Astrocyte Analysis
![Page 2: BY Bhimanathini Venkatsai Sai Kumar Maddula PROJECT#3(b) Astrocyte Analysis.](https://reader036.fdocuments.in/reader036/viewer/2022062519/5697bfae1a28abf838c9c65d/html5/thumbnails/2.jpg)
1. Astrocyte2. Image Segmentation3. Thresholding4. Astrocyte Analysis
– Convert Stack file to 8-bit– Apply Threshold– Segmentation by 3D Viewer– Selection of Seed Point– Overlapping/Touching cell Structure– Apply Singletonize 3D
Contents
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• Astrocyte , are characteristic star-shaped Glial cells in the brain and spinal cord. They are the most abundant cell of the human brain.
Astrocyte
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• Image segmentation is the process of assigning a label to every pixel in an image such that pixels with the same label share certain visual characteristics like colour, texture etc.
• The result of image segmentation is a set of segments that collectively cover the entire image, or a set of contours extracted from the image
IMAGE SEGMENTATION
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• This is method of Image segmentation, where grayscale image thresholding can be used to create binary image.
• There are few thresholding methods based on the information the algorithm manipulates.
Such as:• Clustering based methods• Entropy based methods• Histogram shape based methods• Etc…
Thresholding
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• Load the stack File into ImageJ
File Open Browse Stack File
Astrocyte Analysis:
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• If Stack file is not in 8-bit image format. Convert it into 8-bit image format.
Image Type click 8-bit
Where: Scale 0= Black Scale 128=Medium Gray Scale 255= White
Convert the Stack File to 8-bit image
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![Page 9: BY Bhimanathini Venkatsai Sai Kumar Maddula PROJECT#3(b) Astrocyte Analysis.](https://reader036.fdocuments.in/reader036/viewer/2022062519/5697bfae1a28abf838c9c65d/html5/thumbnails/9.jpg)
• We use Thresholding for detecting edges , counting particals or measuring areas.
Image Adjust select ‘Threshold’
Note: Check ‘Dark Background’ in the Threshold pop-up window and Apply.
Apply Threshold:
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![Page 11: BY Bhimanathini Venkatsai Sai Kumar Maddula PROJECT#3(b) Astrocyte Analysis.](https://reader036.fdocuments.in/reader036/viewer/2022062519/5697bfae1a28abf838c9c65d/html5/thumbnails/11.jpg)
Note: ‘calculate threshold for each image’ should be checked.
![Page 12: BY Bhimanathini Venkatsai Sai Kumar Maddula PROJECT#3(b) Astrocyte Analysis.](https://reader036.fdocuments.in/reader036/viewer/2022062519/5697bfae1a28abf838c9c65d/html5/thumbnails/12.jpg)
• Here 3D Viewer uses Java 3D to provide hardware-accelerated 3D visualization of image stacks as volumes, surfaces and orthoslices.
Plugins Segmentation Click ‘Segment blob
in 3D Viewer’
Segmentation by 3D Viewer
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![Page 14: BY Bhimanathini Venkatsai Sai Kumar Maddula PROJECT#3(b) Astrocyte Analysis.](https://reader036.fdocuments.in/reader036/viewer/2022062519/5697bfae1a28abf838c9c65d/html5/thumbnails/14.jpg)
![Page 15: BY Bhimanathini Venkatsai Sai Kumar Maddula PROJECT#3(b) Astrocyte Analysis.](https://reader036.fdocuments.in/reader036/viewer/2022062519/5697bfae1a28abf838c9c65d/html5/thumbnails/15.jpg)
• Select a seed point as a start (using ‘Point Selections’
Modern image segmentation techniques are
based on PDE (Partial differential equations. The Fiji Plugin provides two PDE based
methods i) Fast Marching ii) Level Sets.
Selection of Seed Point
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![Page 17: BY Bhimanathini Venkatsai Sai Kumar Maddula PROJECT#3(b) Astrocyte Analysis.](https://reader036.fdocuments.in/reader036/viewer/2022062519/5697bfae1a28abf838c9c65d/html5/thumbnails/17.jpg)
• Here we apply Thresholding on binary image stack file then we follow the below steps..
1) Process Binary Watershed
2) Analyze Analyze Particles Outlines Display Result
Overlapping/Touching Cell Structures
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Thank you..!!