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