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registration between label-free and light-sheet arms #14

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mattersoflight opened this issue Apr 14, 2023 · 2 comments · Fixed by #55
Closed

registration between label-free and light-sheet arms #14

mattersoflight opened this issue Apr 14, 2023 · 2 comments · Fixed by #55
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analysis Software development needed for data analysis 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 the registration module in the following iterations.

  1. Extend the deskewing CLI (after merging Generalized deskewing for mantis #6) to compute the rigid transformation in XY and XZ planes between label-free and one fluorescence channel to get rough alignment.
  2. Refine the alignment further with phase correlation or other algorithms as needed.

In this case, it may make sense to register the volumes via writing the Coordination Transformation metadata. @edyoshikun can you link the issue/code snippet on iohub on how to do this?

Looks like @talonchandler can implement (1), and @edyoshikun can review.

@edyoshikun
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I added a PR for the corodinate transformation metadata . Additionally, pointing to the closed issue here

@ieivanov
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We also needs to figure out how to collect the registration data. As LF and LS arms can be focused independently, we'll likely need to collect registration data every time, and allow for Z drift over time. Image-based autofocus that adjusts O3 in each arm may help here.

@ieivanov ieivanov added urgent Problem that needs to be resolved asap analysis Software development needed for data analysis labels Apr 25, 2023
@ieivanov ieivanov linked a pull request Jul 21, 2023 that will close this issue
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analysis Software development needed for data analysis urgent Problem that needs to be resolved asap
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