cellpose
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MouseLand
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
**Describe the bug** If the `CELLPOSE_LOCAL_MODELS_PATH` is set to the current working directory (cwd), then the model is downloaded properly but the size model fails to download and leads to...
**Describe the bug** A clear and concise description of what the bug is. **To Reproduce** Steps to reproduce the behavior: 1. Go to Brightness & contrast in QuPath 0.5.0 2....
Dear all, I wanted to make a prediction on the 3D stack, and I found that the `stitching` method works better than `do_3D`. However, I would like to use a...
**Install problem** ** TORCH CUDA version installed and working. ** This plugin does not support propagateSizeHints() **Environment info** _libgcc_mutex 0.1 main _openmp_mutex 5.1 1_gnu blas 1.0 mkl brotli-python 1.0.9 py38h6a678d5_8...
# Use a Napari-labels-like data format to reduce the size of Cellpose mask output before stitching I was working with a large (14 GB) image stack and segmented it in...
**Describe the bug** ```python model = models.Cellpose(gpu=False, model_type="nuclei") masks, _, _, _ = model.eval(image, diameter=diameter) ``` If < ~80 Gb of memory provided for the job, then `masks` is `None`....
Hi there, A t_axis option in [cellpose.models.Cellpose.eval](https://cellpose.readthedocs.io/en/latest/api.html#cellpose.models.Cellpose.eval) would be awesome.
When applying a custom model to a ~3 GB 3D data set (1000x1024x ~1500 slices, 16-bit grayscale), I encountered issues with running out of memory. I've seen several issues on...
**Describe the bug** the file [vit_sam.py](https://github.com/MouseLand/cellpose/blob/v4.0.4/cellpose/vit_sam.py) contains the line ```python torch.backends.cuda.matmul.allow_tf32 = True ``` right within the imports at the top. This is globally changing the pytorch configuration, which can...
Hi @carsen-stringer , Hi @mrariden , Hi all, **Describe the bug** if the images have a lot of pixels per cells (here diameter 1000) the results with **cpsam** looks pixelated...
