cellpose
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MouseLand
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
At run_Cellpose-SAM.ipynb file, both io.imsave() and io.save_rois() should not return anything since the API specifies that these two functions return None. Also, the `mask[i]` is missing in the io.imsave() function....
**Describe the bug** I am segmenting a H&E image, the algorithm runs for a while, and then suddenly, the GPU usage spikes, and I get a cda OOM error. Reducing...
Cellpose-SAM excels at 3-D **inference**, but **training** still expects 2-D slices. This forces users to: * pre-slice every z-stack, losing volumetric anisotropic sampling context for learning model flow embeddings *...
**Describe the bug** A custom-trained model produces widely different results between cellpose-4 (0 cells identified) and cellpose-3 (66 cells identified). I'm not sure if this is expected behaviour with the...
Hello, I used the "cytosam" model to segment my spatial molecular imaging data and the results look great! I was wondering if any variant of the cellposeSAM models are able...
Hi, I’m using the notebook from the Cellpose github ([cellpose/notebooks/train_Cellpose-SAM.ipynb at c68d52e08162430c82677bb0bab66a68b95f1898 · MouseLand/cellpose · GitHub](https://github.com/MouseLand/cellpose/blob/c68d52e08162430c82677bb0bab66a68b95f1898/notebooks/train_Cellpose-SAM.ipynb)) to train my dataset on Google Colab. Problem: the GPU RAM is increasing during...
**Install problem** I am trying to use train my own model for segmentation of my cells. But I am unable install model zoo. The only segmentation module that appears is...
**Describe the bug** I'm running the run_Cellpose-SAM.ipynb file in colab with gpu, but got the TypeError: imsave() missing 1 required positional argument: 'arr' . To resolve this issue, I double...
Moved log file up 1 line so that it logs the correct variable replaced 2 instances of 'cpsam' with _DEFAULT_MODEL, functionality unchanged.
Allow exporting masks to JSON for better model interoperability. There are a few schemas but maybe the most popular one? Suggestions are appreciated. **Describe alternatives you've considered** Use another tool...
