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Visualize similar cells on a 2D plot using t-SNE

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Kafri-Lab/Cell-t-SNE

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Visualize Single Cells Using t-SNE

t-SNE Result Plot:

tsne output

Color Legend (Ground Truth)

  • #00dd0e Green cells are cytoplasm stained only and are correctly grouped by t-SNE.
  • #ff0000 Red cells are peroxisome stained only and are correctly grouped by t-SNE.
  • #7c7c7c Gray cells are nucleus stained only and are correctly grouped by t-SNE.
  • #0f6afc Blue cells are whole cell stained and the sample size is too small to see a t-SNE group.

Project Layout

Directory or file Description
"Visualizing with t-SNE.ipynb" Main code file! Contains lots of practice and a final section which produces the above t-SNE image
"barcode_images/" 1,571 cropped, rotated, and masked single cell images used in t-SNE. Each cell is barcoded with a different stain localization within the cell

Project Status

I'm hoping to clean up the code. Open an issue if you need help.

Futher reading about t-SNE...