cellpose
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MouseLand
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
Thanks for the nice software. I trained a model in the GUI and I was trying to now use a jupyter notebook to apply it to multiple images. I tried...
Hi, I want to use cellpose on some rather large .tif files of sizes ranging from 1GB-10GB. They are **2-d RGB images**. I have a Tesla T4 GPU and 32GB...
I am training a model using the GUI. When I train the model using my annotated set of images with nuclei as an initial model all is well. However, when...
It often happens that people are interested in obtaining cell outlines plus nuclei in order to obtain compartment-based measurements **Describe the solution you'd like** Considering cellpose just added a new...
When I try to save masks after manual refinement (addition/deletion of masks) of cyto3 segmentation results as an ImageJ ROI zip file, I get following error: "ValueError: zero-size array to...
torch version 2.2.2 cellpose version 3.0.7 I get an AttributeError when I call train_seg function. I use the latest version of cellpose. path_to_new_model = train_seg(old_model, train_data=training_images, train_labels=training_masks, test_data=images_test, test_labels=masks_test, batch_size=8,...
**Describe the bug** As described above when training a new finetuned model starting from nuclei everything appears to work correctly during training. it shows the following ```bash 2024-03-26 15:47:24,727 [INFO]...
The segmentation of 3d tif stacks is taking 5-6 minutes to process 1 image when --no_norm is used. When the same stacks are processed without --no_norm argument then it takes...
**Describe the bug** I wrote a script to denoise tif stacks using the new DenoiseModel class from Cellpose 3. It works great but there appears to be an issue with...
I am trying to run Cellpose 2.0 through a Jupyter notebook (have used the same one previously without issue and have not changed any code). The block dedicated to generating...
