[BUG] Cellpose 3 using GPU macOS M1 #1034
Comments
|
sorry there was a typo in the readme, can you please use python=3.10 and |
|
Thanks a lot! I've tried what you suggest but I got this error: A module that was compiled using NumPy 1.x cannot be run in If you are a user of the module, the easiest solution will be to |
|
Hmm which module is having the issue? |
|
I found these lines: |
|
I have tried to downgrade Numpy to 1.23.5. but still GPU cannot be used and without the use of GPU the trained model does not detect cells. |
|
I am having the same issue concerning not being able to get any segmentation objects with the GPU on a mackbook pro M1. When I try running the commands I get the following error suggesting that the backend is failing. NotImplementedError Traceback (most recent call last) File ~/mambaforge/lib/python3.10/site-packages/cellpose/models.py:453, in CellposeModel.eval(self, x, batch_size, resample, channels, channel_axis, z_axis, normalize, invert, rescale, diameter, flow_threshold, cellprob_threshold, do_3D, anisotropy, dP_smooth, stitch_threshold, min_size, max_size_fraction, niter, augment, tile_overlap, bsize, interp, compute_masks, progress) I tried installing the OratHelm clone and it allows me to run the samples with GPU on macbook pro M1 no problem but I get the warning: "/Users/user/mambaforge/lib/python3.10/site-packages/cellpose/dynamics.py:189](https://file+.vscode-resource.vscode-cdn.net/Users/solivanriv/mambaforge/lib/python3.10/site-packages/cellpose/dynamics.py:189): RuntimeWarning: invalid value encountered in divide Unfortunately, the segmentation results from the most updated version are a bit more accurate than the OratHelm fork. I have a lot of images and GPU support would be ideal with the most recent version, but I cannot seem to pinpoint a solution. |
|
I am also encountering a problem with version 3.1.0: since the update, it is impossible to use the GPU either to calibrate the diameter or to segment. I have the following error: On the same configuration (M3 Pro, python 3.9.13, torch 2.5.1), after reinstalling Cellpose 3.0.11, it works correctly and I have no warnings on my side. For the moment, if it helps, this version can be installed with |
|
darn, I wish Apple would help pytorch implement all these functions for MPS! I upgraded the mask computation using sparse matrices, and they must not be supported. I will default to the old mask computation for MPS until they implement it |
|
@OratHelm thanks for the suggestion! Going back to 3.0.11 worked for me! I am seeing a small error coming form the dynamics.py stating: "RuntimeWarning: invalid value encountered in divide I guess that this is emerging from a division by zero. Sounds like this should not alter my results though, segmentation images look fine. @carsen-stringer, thanks! Hopefully, they will implement this soon! |
I had the same bug using cellpose 2 to detect cells after the training of model (2D) so I decided to install Cellpose 3 on my macOS M1, using Anaconda. I follow the protocol posted on GitHub
https://github.com/MouseLand/cellpose?tab=readme-ov-file#option-1-installation-instructions-with-conda
All models fail to detect cells using the GPU option. When I use Cellpose + track mate, the GPU option does not detect any cells.
Thanks for your help!
The text was updated successfully, but these errors were encountered: