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Implement possibility to refine masks after CellPose segmentation #47

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MaximLippeveld opened this issue Feb 3, 2022 · 1 comment
Open

Implement possibility to refine masks after CellPose segmentation #47

MaximLippeveld opened this issue Feb 3, 2022 · 1 comment
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segmentation Relating to segmentation

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@MaximLippeveld
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CellPose produces a mask for one channel only. Running CellPose for every channel is too computationally intensive. This can be solved by using CellPose to get a mask that covers the entire cell, and subsequently refining that mask per channel.
@MaximLippeveld MaximLippeveld added the segmentation Relating to segmentation label Feb 3, 2022
@MaximLippeveld
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Refining the mask within the parent patch proved difficult, because very little context is available around the cell. It should be feasible though, so I will revisit this in the future.

Currently it is only possible to generate a new CellPose mask for a second channel. These segment are then assigned to the parent cell based on overlap.

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