Astrocyte Analysis
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Astrocyte Analysis Jing Mao
description
Astrocyte Analysis. Jing Mao. Goals. Extract, classify and count individual glial cells Find seed points to start segmentation Terminate segmentation for overlapping glial cells Measure degree of astrocyte overlap with vessels in secondary channel Percentage of total cell overlap - PowerPoint PPT Presentation
Transcript of Astrocyte Analysis
Astrocyte AnalysisJing Mao
Goals• Extract, classify and count individual glial cells• Find seed points to start segmentation• Terminate segmentation for overlapping glial cells
• Measure degree of astrocyte overlap with vessels in secondary channel • Percentage of total cell overlap• What part of the cell overlaps • Relate this to groupings of cells
Preprocess• Image-stack-tools-stack splitter• Split three channels
Preprocess
Channel 1 Channel 2
Preprocess• Using existing plugin adaptive Thr• Extract features from background
Preprocess• Process-Noise-Despeckle• Analyze-Analyze Particles
Channel 1 Channel 2
Analyze • Build plugin to compute the percentage of cell overlap
Channel 1
height 78 slices
Channel 2 width
Analyze
Channel 1 Channel 2
Two channels
Total slices
Width and height for each slice
Total number of pixels with white in channel 1 and 2
Overlap in channel 1 and channel 2
Mark overlap area to red
Results
White pixels Overlap Overlap Percentage
Channel1 128519104374089
34%
Channel2 19631155 22%
Results
Cell Overlap in Channel 1
