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Extracting regionprops from multichannel image #186

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nthndy opened this issue Oct 31, 2022 · 2 comments
Open

Extracting regionprops from multichannel image #186

nthndy opened this issue Oct 31, 2022 · 2 comments
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@nthndy
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nthndy commented Oct 31, 2022

When supplying btrack.utils.segmentation_to_objects with a multichannel image, an error is raised regarding the conversion of the regionprops table into dictionary format.
This is because regionprops is confused by use_weighted_centroid and tries to record a value for each channel for every property, when it should only be doing that for the image intensity values.
So this error can be fixed by just setting this parameter to False.
I added an explainer in the docstring here, not sure if you'd like me to do a pr:
https://github.com/nthndy/BayesianTracker/blob/bdf6667a301ecdaf15da37a916aadf23c4ac620a/btrack/_localization.py#L151
Lmk if you'd rather a proper fix, like a error raise or something.

@quantumjot quantumjot added the bug label Nov 1, 2022
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Feel free to do a PR!

@paddyroddy paddyroddy moved this to 🗒 Backlog in btrack-napari Mar 8, 2023
@quantumjot
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Could be a good use case for:
alan-turing-institute/pixelflow#3

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