brainglobe / cellfinder

Automated 3D cell detection in very large images

Home Page:https://brainglobe.info/documentation/cellfinder/index.html

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

Update cell classification network

adamltyson opened this issue · comments

For many reasons the existing cell classification network (and associated helper functions) is suboptimal:

The use of TensorFlow is also causing headaches:
#293

I think now is the time to fix this. Previously I've raised brainglobe/cellfinder-core#220 and brainglobe/cellfinder-core#221. But essentially my idea is to update the code (refactoring as we go) to Keras 3.0 which is now out.

It would also be cool to address this in a way that would support:

First steps (chat with @IgorTatarnikov)

  • migrate to Keras 3.0
    • verify accuracy of results (via tests)
    • verify no performance differences (via time/memory benchmarks)