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
