cellpose
cellpose copied to clipboard
MouseLand
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
## Before you fill out this form: **Did you review the FAQ?** - [ ] Yes, I reviewed the FAQ on the [cellpose ReadTheDocs](https://cellpose.readthedocs.io/en/latest/faq.html) **Did you look through previous (open...
Hi, I am using Cellpose 4 GUI 3D mode on a 3D image. However, it does not allow me to manually draw circles after getting the automate results, or specifically,...
Hi, for a project of mine I needed to scale cellpose on a SLURM cluster. To make the topic a little more interesting, the [cluster](https://docs.mpcdf.mpg.de/doc/computing/viper-gpu-user-guide.html) I have at hand has...
I have 17 spatial transcriptomics samples (1 sample shown) with paired H&E images. I am looking to predict cell types from H&E, and for that, I finetuned Cellpose-SAM model for...
**Describe the bug** When I try to train a new model, an error occurs when saving. **To Reproduce** Steps to reproduce the behavior: I followed the train new model instructions....
**Title** [BUG] Cellpose model exported from 3.1.1.1 silently fails to work properly on latest 4.0 version **Describe the bug** A custom, fine-tuned model (`cyto3_train0327`) exported from Cellpose version **3.1.1.1** does...
**Describe the bug** Disclaimer, this is my first time using cellpose and I am a relatively novice coder. I installed the GUI for cellpose v 4.0.8 without issues and am...
**Describe the bug** When segmenting a 3D z-stack volume with shape (24, 2048, 2048) and `diameter = 20` the image is correctly resized to (24, 3072, 3072) before running `_run_net`....
Hello, I was confused to see that the default training pipeline does not save state_dicts at lowest validation loss? Also I am curious why there is no validation splitting? There...
**Is your feature request related to a problem? Please describe.** I’m using `distributed_segmentation` on large 2D multi-channel images with shape (C, H, W). To make the Zarr array tile cleanly,...
