Open FranJGonCal opened 1 month ago
is this image a z-stack or a single image? does it show up correctly in the GUI? if you have a z-stack then you want to open cellpose with python -m cellpose --Zstack
is this image a z-stack or a single image? does it show up correctly in the GUI? if you have a z-stack then you want to open cellpose with
python -m cellpose --Zstack
It's a single image.
Trying different approaches, I found a way in which It's run correctly. When uploading the image to the program, I was using the "use GPU" option and the problem which I was commenting appeared. However, if I do not choose this option, the progrma runs correctly.
Anyway, thanks so much for your answer.
Weird thanks for the update, somehow the GPU torch version isn't work, I would also try updating to the latest version v3.0.11 (pip install cellpose --upgrade
) and upgrading torch in the same way
GPU in this case is MPS
I am also having this problem, only when running on GPU (CPU works OK). The error trace is:
`./run_segmentation.sh
2024-09-30 13:35:19,050 - INFO - TORCH MPS version installed and working.
2024-09-30 13:35:19,050 - INFO - >>>> using GPU (MPS)
2024-09-30 13:35:19,050 - INFO - >> nuclei << model set to be used
2024-09-30 13:35:19,153 - INFO - >>>> loading model /Users/merrickpiersonsmela/.cellpose/models/nucleitorch_0
2024-09-30 13:35:19,223 - INFO - >>>> model diam_mean = 17.000 (ROIs rescaled to this size during training)
2024-09-30 13:35:23,835 - INFO - channels set to [0, 0]
2024-09-30 13:35:23,835 - INFO - ~ FINDING MASKS ~
/Users/merrickpiersonsmela/miniforge3/envs/imageprocessing2/lib/python3.11/site-packages/cellpose/dynamics.py:189: RuntimeWarning: invalid value encountered in divide
mu /= (1e-60 + (mu2).sum(axis=0)0.5)
Traceback (most recent call last):
File "/Users/merrickpiersonsmela/Documents/Church_Lab/oogenesis/Images/Segmentation_analysis/2024-09-30_meiosis_BOLL_RNA/../src/segmentation.py", line 93, in
IndexError: index 2834 is out of bounds for axis 1 with size 2834`
Having the same issue on MacOS, cellpose 3.0.11, 2D images (IndexError in line 194 dynamics.py
). However the issue went away when I reverted using pip install cellpose==3.0.8
. Happy to share more info if useful.
hmm nothing in that function has changed in the past 7 months.
can you upgrade to the latest github version? pip install git+https://github.com/mouseland/cellpose.git
if that doesn't work, could you please check if masks_padded is a reasonable size? https://github.com/MouseLand/cellpose/blob/52f75f9636250979dcff48da18d24aaff41c2c86/cellpose/dynamics.py#L159
Hello, I'm new to cellpose and I find an error when upload my file to the program. When I upload an RGB image and run the cyto3 model to segment the image (to later train a custom model) using the gui, an error NET ERROR: index 1024 is out of bounds for axis 1 with size 1024 appears, so no mask are found, and also no segmentation is performed. I don't really know if I need to manually draw the mask of the cells that I want to segment before running the cyto3 model.