heatmaps in DSA

HistomicsTK
1

Hello all, so far I have been using DSA to gather annotations and to displaying my predictions (as polygons). I would like however display my predictions as heatmaps, pretty much as sated in this old gitter msg :

Screenshot 2021-06-14 at 10.19.08
Screenshot 2021-06-14 at 10.19.081550×382 71.3 KB

Thanks for any help!

2

Heatmaps can be upload like any other annotation. There are two formats: see large_image/annotations.md at master · girder/large_image · GitHub and the section below it.

  • David
3

Thanks David! So if I have a heatmap for the whole slide, should I list all the pixels? Wouldn’t that be a lot?

4

Although it is somewhat slow to load, it should work – I’m not sure I’ve seen it used with more than ~10,000,000 points though. There is a grid form which is more compact if you are doing that (large_image/annotations.md at master · girder/large_image · GitHub). In other projects, users have downsampled their heatmaps by some factor, storing only every second or forth value.

5

That makes sense! Thanks a lot David