1. PROJECT#3(b) Astrocyte Analysis
BY Bhimanathini Venkatsai
Sai Kumar Maddula

2. Contents Astrocyte Image Segmentation Thresholding 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

3. Astrocyte
Astrocyte , are characteristic star-shaped Glial cells in the brain and spinal cord. They are the most abundant cell of the human brain.

4. IMAGE SEGMENTATION
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

5. Thresholding
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…

6. Astrocyte Analysis: Load the stack File into ImageJ
File  Open Browse Stack File

7. Convert the Stack File to 8-bit image
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

9. Apply Threshold:
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.

11. Note: ‘calculate threshold for each image’ should be checked.

12. Segmentation by 3D Viewer
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’

15. Selection of Seed Point
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.

17. Overlapping/Touching Cell Structures
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

20. Thank you..!!