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Add support for other types of projections on ImageStack #1302

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kevinyamauchi opened this issue May 3, 2019 · 4 comments · Fixed by #1342
Closed

Add support for other types of projections on ImageStack #1302

kevinyamauchi opened this issue May 3, 2019 · 4 comments · Fixed by #1342
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@kevinyamauchi
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kevinyamauchi commented May 3, 2019

Proposal

I think it would be useful to expose other methods of projecting along axes for ImageStack (e.g., DataArray.sum() and DataArray.mean()). This would add support the ExFISH case for projecting across (R, C) before spot segmentation (#1301).

Implementation

Some possibilities:

  1. I think the thing that is the least work is to make a filter, Filter.Project that takes projection type as an input argument. This could replace Filter.MaxProject.
  2. We could do the same as (1), but make it a method of ImageStack. I think a lot of the notebooks would have to be updated, as they use ImageStack.max_proj().
  3. We could also make one filter component per projection type, but this seems too granular.

As a related aside: I think there should be only one way to max project (i.e., ImageStack.max_proj() and Filter.MaxProject are redundant).

Thoughts, @dganguli , @ambrosejcarr ?

@ttung
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ttung commented May 7, 2019

For reasons of API stability, we should not remove Filter.MaxProject for a number of releases after we implement Filter.Reduce.

ImageStack.max_proj() should be a hidden method, IMO.

@kevinyamauchi
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@ttung, is Filter.Reduce a planned component or a proposed name for this component?

@ttung
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ttung commented May 9, 2019

I'm proposing it. :)

@kevinyamauchi
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Sounds good, @ttung . I took a crack at it in #1342. I still need to add tests, but feel free to check it out if you're curious.

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