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kreshuklab / plant-seg

A tool for cell instance aware segmentation in densely packed 3D volumetric images
https://kreshuklab.github.io/plant-seg/
MIT License
96 stars 31 forks source link

Problem running plant-seg on batch mode #121

Closed lcferme closed 6 months ago

lcferme commented 2 years ago

Hello,

When I try to run plant-seg on multiple images in a folder, after completing the predictions for the first image, I get the following message: [...] File "h5py\_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py\_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py\h5f.pyx", line 106, in h5py.h5f.open OSError: Unable to open file (file signature not found)

This happens both when I use the GUI and when I try to run plant-seg from the terminal. Do you know what is the problem? Thanks!

Lucrezia

lorenzocerrone commented 2 years ago

Hi Lucrezia,

I hope I can help you with your request.

From the error message it seems that the error comes from a wrongly formatted or corrupted h5 file. Could you try to open the same h5 file using another software like fiji?

When does the error occur? (in the preprocessing, in the cnn predictions or in the segmentation)

Best, Lorenzo

qin-yu commented 8 months ago

Hi @lcferme, thanks for reporting. Are you still using PlantSeg? The software has changed a lot. Maybe I'll close this issue if there is no more follow-up.