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set up about custom_malis HOT 6 OPEN

constantinpape avatar constantinpape commented on June 28, 2024
set up

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constantinpape avatar constantinpape commented on June 28, 2024

@remrace
Is your issue resolved?
Regarding the conda install: unfortunately I failed to upload the package to my channel.
If you still need it let me know.
But be advised: this package is not really tested.

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remrace avatar remrace commented on June 28, 2024

@constantinpape
The setup is fine now, but as I contacted you, about the affinities and groundtruth input for the forward pass, I'm not quite understand the requirements for the shapes of those input, especially for the 2D image case.

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constantinpape avatar constantinpape commented on June 28, 2024

For a 2D image of shape (s_x, s_y) you will need to input a segmentation of shape (s_x, s_y) and affinities of shape (2, s_x, s_y). Here the first affinity channel encodes the affinities in x-direction, the 2nd channel the affinities in y-direction.

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remrace avatar remrace commented on June 28, 2024

I understand that the affinities is the edges between two pixels? Then, in x-direction, the affinities should be (s_x - 1, s_y) and in y-direction, (s_x, s_y - 1) ? Should I then padding these with 1 extra row/col of zeros?

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constantinpape avatar constantinpape commented on June 28, 2024

yes, exactly

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remrace avatar remrace commented on June 28, 2024

Thanks @constantinpape , if possible (if you have time to write some explanation), I'd like to gain a deeper understanding of how and why MALIS works.

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