Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Cannot use predict slide for MIL model #365

Open
jziggles opened this issue Apr 29, 2024 · 0 comments
Open

Cannot use predict slide for MIL model #365

jziggles opened this issue Apr 29, 2024 · 0 comments
Labels
bug Something isn't working

Comments

@jziggles
Copy link

Description

The "predict_slide" function in slideflow studio does not work. I have been using the magnification value in the tile_um variable during tile extraction. The slides (TCGA library for ER status by IHC) appear to have different tile_um sizes ranging from 497 to 505 uM when they are loaded in slideflow. Is this variable nature the problem?

To Reproduce

Steps to reproduce the behavior:

  1. Load project
  2. Load MIL model
  3. Load slide that has been run in MIL model w/ attention values
  4. Click predict slide

Error message in slideflow studio
MIL model tile size (tile_px = 500, tile_um = 10x) does not match the currently loaded slide (tile_px = 500, tile_um=497)

Expected behavior

I want to be able to predict the slide and overlay attention values.

Environment:

  • Slideflow Version (e.g., 1.0): 2.3.1
  • OS (e.g., Ubuntu): Red Hat 8
  • How you installed Slideflow (pip, source): pip
  • Python version: 3.9
@jziggles jziggles added the bug Something isn't working label Apr 29, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working
Projects
None yet
Development

No branches or pull requests

1 participant