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teamtomo / membrain-seg

membrane segmentation in 3D for cryo-ET
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Training from scratch: 3D Coordinates #33

Closed virlyananda closed 9 months ago

virlyananda commented 10 months ago

Hello,

Thanks for releasing this package, the v10 pre-trained model works great on our tomogram. However, as we try to implement training from scratch based on our own data, I found this error: Screenshot from 2023-08-21 11-32-29 Screenshot from 2023-08-21 11-30-27

I followed the tutorial both from the repository and video, it doesn't seem that I'm missing anything? Tomogram path is based on the pre-processed pixel matching step, and segmentation path is based on the binary output from pre-trained model prediction (segmentation).

When I tried to locate 3D coordinates on IMOD, it works fine. If I'm missing something, could you please point out the possible issue? Thanks.

Best, Virly

LorenzLamm commented 10 months ago

Hi Virly, Thanks for your feedback on this! I see that your z-coordinate is 35. Since the size of the extracted patches is (160,160,160), this may be too small of a coordinate. In order to extract patches properly from the tomogram, the coordinates should be at least 80 voxels apart from the tomogram boundaries.

Could this be the issue?

Best, Lorenz

virlyananda commented 10 months ago

Hi Lorenz,

Thanks for your response. That could be it. I relocated the coordinate point further away from the tomogram boundaries and it's working now.

Best Regards, Virly