by bhimanathini venkatsai sai kumar maddula project#3(b) astrocyte analysis

BY Bhimanathini VenkatsaiSai Kumar Maddula

PROJECT#3(b)Astrocyte Analysis

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

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

Astrocyte

• 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

• 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

• Load the stack File into ImageJ

File Open Browse Stack File

Astrocyte Analysis:

• 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

• 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:

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

• 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

• 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

• 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

Thank you..!!