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implement viewer #12

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mattersoflight opened this issue Apr 14, 2023 · 3 comments · May be fixed by #30
Open

implement viewer #12

mattersoflight opened this issue Apr 14, 2023 · 3 comments · May be fixed by #30
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urgent Problem that needs to be resolved asap

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@mattersoflight
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mattersoflight commented Apr 14, 2023

I suggest building a viewer in iterations as follows:

  1. view raw data: label-free in micro-manager, light-sheet skewed volumes in napari.
  2. view deskewed volumes: on-the-fly deskewing. On-the-fly deskewing can follow this PR (Generalized deskewing for mantis #6).
    Try this plugin works.
  3. view overlays of registered phase and deskewed volumes in napari (after parallelized deskew and phase deconvolution  #13 ).

Looks like @ieivanov is ready to implement (1) and @edyoshikun can review.

@mattersoflight mattersoflight changed the title viewer implement viewer Apr 14, 2023
@ieivanov
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  1. will not work - there is no way to view PM data in MM. I think Henry tried to develop something for that, but it hasn't worked for me. We may be able to use the PM NDViewer for LF data, but if we can view LS data in napari, then it's just as easy to view LF data in napari as well.

My plan is to start with on-the-fly viewing of LF and LS raw data in napari in a very similar fashion to how the native PM napari viewer works. We'll just be opening two arrays rather than one.

The next step would be to view deskewed LF volumes. I agree that the napari-ndtiffs plugin may be helpful here (tho it didn't work for me right away). This is decoupled from #13 as we'll be using the native napari transform functionality, rather than resampling with skimage and saving the deskewed array.

Viewing the registered volumes would be the ultimate goal. We'll need to figure out how to do registration first in #14

@mattersoflight
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mattersoflight commented Apr 15, 2023

there is no way to view PM data in MM.

Is the data acquired with dragonfly-automation also written in NDTIFF format? I am able to open the whole dataset with @ziw-liu's Micro-Manager 2 apptainer.

image

My plan is to start with on-the-fly viewing of LF and LS raw data in napari in a very similar fashion to how the native PM napari viewer works. We'll just be opening two arrays rather than one.

Even if we can Micro-Manager to view label-free data, viewing all the data in napari makes even more sense. We should try this route and see how it works.

@ieivanov
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Just to confirm, the data in your example is written with MM rather than PM

@ieivanov ieivanov added the urgent Problem that needs to be resolved asap label Apr 25, 2023
@ieivanov ieivanov linked a pull request Apr 30, 2023 that will close this issue
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