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Allow specifying the mask and bbox keys in the GraphArrayView#293

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cmalinmayor wants to merge 2 commits into
royerlab:mainfrom
cmalinmayor:multiple-masks-per-node
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Allow specifying the mask and bbox keys in the GraphArrayView#293
cmalinmayor wants to merge 2 commits into
royerlab:mainfrom
cmalinmayor:multiple-masks-per-node

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@cmalinmayor

@cmalinmayor cmalinmayor commented May 22, 2026

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We want to store two masks for each cell - the whole membrane and the nucleus segmentations - and display them both as GraphArrayViews in napari. This edit should keep the default behavior of "mask" and "bbox" if not specified, but allow you to specify.

Is there anywhere else in the repo where a single mask and bbox per node is assumed that I should be aware of to make sure I don't break any default behavior? @TeunHuijben @JoOkuma (tagging cause I can't request reviewers)

Second edit: immediately found more places when I tried to run a slightly different script, new commits coming 🙃

@cmalinmayor cmalinmayor force-pushed the multiple-masks-per-node branch from 7c56781 to 68bbb6a Compare May 22, 2026 14:29
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Force pushed to rebase onto rc3, so I can actually run tests without running into #294

@TeunHuijben TeunHuijben requested a review from JoOkuma May 28, 2026 17:59
@TeunHuijben

TeunHuijben commented May 29, 2026

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@cmalinmayor, let's try this on your side without the rebase, but using the latest tracksdata release, and funtracks main

@JoOkuma

JoOkuma commented Jun 1, 2026

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@cmalinmayor, I'm returning from vacation. Sorry for the late reply.

Multiple masks should definitely work, as long as you provide the correct non-default attribute name when displaying the alternative masks.

I'm going to Janelia on Jun 11th, happy to team up and help with any other issues you're having.

@cmalinmayor

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Multiple masks should definitely work, as long as you provide the correct non-default attribute name when displaying the alternative masks.

Provide them where? The defaults are currently hard-coded into the GraphArrayView on main, which is what this PR changes.

I'm going to Janelia on Jun 11th, happy to team up and help with any other issues you're having.

Definitely! I'm finally diving deeper into the tracksdata world, and I think I can have more intelligent questions now. Would love to pair program a bit while you are here.

@cmalinmayor cmalinmayor force-pushed the multiple-masks-per-node branch from 230a8e5 to ada3f73 Compare June 3, 2026 23:30
@JoOkuma

JoOkuma commented Jun 5, 2026

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@cmalinmayor

Provide them where? The defaults are currently hard-coded into the GraphArrayView on main, which is what this PR changes.

Agreed, your PR is necessary.

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3 participants