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Next steps: segmentation & registration #3

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1 of 5 tasks

constantinpape opened this issue Apr 23, 2024 · 0 comments

Open

1 of 5 tasks

Next steps: segmentation & registration #3

constantinpape opened this issue Apr 23, 2024 · 0 comments

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constantinpape commented Apr 23, 2024 •

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Segmentation:

Implement MoBIE integration
Implement feature extraction to measure intensity expression per segmented cell. (This should be rather straight-forward: use the bounding boxes computed by MoBIE to parallelize this via regionprops)
Precompute data nomalization parameters for the full volume to avoid artifacts due to hot pixel regions.
Implement hyperparam search on val set (integrate this directly in torch_em and use here)

Registration:

Setting grid positions correctly from Flamingo Metadata

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