search

gitter-lab / pharmaco-image

MIT License
1 stars 0 forks source link

Use t-SNE to explore more images #1

Closed xiaohk closed 1 year ago

xiaohk commented 6 years ago
  1. Use t-SNE to visualize the extracted features from more plates
  2. Test on single cell images
agitter commented 6 years ago

If we find the same results - that the images do not separate by compound in the t-SNE plot - we could also construct an experiment where the images should look different from one another. That might involve identifying compounds in advance that are known to have a strong effect on the cells using prior knowledge about the mechanism of action and then visualizing the network-transformed images for those compounds instead of the set of compounds on a plate.

xiaohk commented 6 years ago

aedebfeeef977e41038bde2732009e9c688d9746 adds result of all t-sne plots of 16 plates.

There are some interesting plots:

interesting

I visualized j16 in plate 24280. It looks there are few cells in the image:

j16