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Export annotations in Napari-compatible format #28

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hannahker opened this issue Jul 11, 2023 · 1 comment · Fixed by #49
Closed

Export annotations in Napari-compatible format #28

hannahker opened this issue Jul 11, 2023 · 1 comment · Fixed by #49
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@hannahker
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hannahker commented Jul 11, 2023

Based on outputs of #25

Annotations should be associated with a given image slice. So when multiple slices have annotations, the output should be 3-dimensional, rather than flattened into 2D.

Also include in the output:

@hannahker hannahker added enhancement New feature or request prototype To be included in the initial prototype labels Jul 11, 2023
@hannahker hannahker added this to the Prototype App milestone Jul 13, 2023
@hannahker hannahker removed the prototype To be included in the initial prototype label Jul 13, 2023
@danton267 danton267 self-assigned this Jul 19, 2023
@danton267 danton267 linked a pull request Jul 20, 2023 that will close this issue
@hannahker
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hannahker commented Jul 20, 2023

Notes on full vs sparse array? For just the annotations, it is likely that we can just export a sparse array across slices - data isn't required where there is no labelling. Necessary information is about which slice number is labelled. This is also input into the ML model.

Also think about the situation where someone might want to download the full array once it has been annotated - the size might not be that big if a large number of pixels are 0, since this could likely be compressed pretty easily.

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