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Support processing 3D over time with Cellpose 3 and Cellpose 4.#66

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tinevez wants to merge 16 commits into
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5d-images
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Support processing 3D over time with Cellpose 3 and Cellpose 4.#66
tinevez wants to merge 16 commits into
mainfrom
5d-images

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@tinevez tinevez commented May 18, 2026

If we receive such an input, we process timepoint by timepoint, and write results in a pre-allocated image.

@tinevez tinevez marked this pull request as draft May 18, 2026 11:53
@tinevez tinevez changed the base branch from main to programmatic-unit-tests May 18, 2026 11:53
tinevez and others added 15 commits May 18, 2026 16:19
Cellpose output are now stored in a specialized class, simply
made of two fields (labels and flows). We know that the flows
will always be uint8. Labels maybe either uint16 or uint32,
hence the generics.
This is specialized class, with default visibility that runs Cellpose.
This class exists so that we can write results in a pre-allocated
output data structure.

Why this class? Normally we can run Cellpose on up to 3D or 2D+T
images, with or without C. As soon as we have 3D images over time
as input, Cellpose will crash. One solution is to have Cellpose
process one time-point after another, writing the results of
processing one time-point in a pre-allocated output data structure.
This class is made to support this approach.

Note that it does not support 5D inputs itself.
When we have such inputs, process one time-point after another,
writing the results in a pre-allocated data structure.
Useful to quickly figure whether Cellpose receives the right
time-point.
Base automatically changed from programmatic-unit-tests to main May 18, 2026 15:47
@tinevez tinevez marked this pull request as ready for review May 18, 2026 15:47
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2 participants