brainglobe / cellfinder

Automated 3D cell detection in very large images

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

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Consider moving away from TensorFlow

adamltyson opened this issue · comments

TF is causing us some headaches, namely lack of support for Windows, and not being on conda-forge. There are other options, but PyTorch seems to be the leading candidate currently. It's on conda-forge, seems fairly easy to install, and it's now part of the Linux Foundation (so can't be killed off by Meta).

I don't know how easy the TF->PyTorch transition would be, but the 3D ResNet here isn't that complicated. A re-write may be a way of speeding things up.

I remember someone had started looking into this (and reported some speedups), but I can't remember who!

I remember someone had started looking into this (and reported some speedups), but I can't remember who!

It was @noisysky! - https://github.com/noisysky/fastai-examples

I wonder if keras-core (soon to be keras 3.0) is a potential solution? keras is on conda-forge, and if the tensorflow backend requirement was removed, we could use pytorch without changing much of the classification code.