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Astrocyte Analysis

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

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Astrocyte Analysis

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  1. Astrocyte Analysis Jing Mao

  2. 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

  3. Preprocess • Image-stack-tools-stack splitter • Split three channels

  4. Preprocess Channel 1 Channel 2

  5. Preprocess • Using existing plugin adaptive Thr • Extract features from background

  6. Preprocess • Process-Noise-Despeckle • Analyze-Analyze Particles Channel 1 Channel 2

  7. Analyze • Build plugin to compute the percentage of cell overlap 78 slices height width Channel 1 Channel 2

  8. Analyze Channel 1 Channel 2

  9. 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

  10. Results

  11. Results Cell Overlap in Channel 1

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