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AllenNeuralDynamics / aind-ophys-motion-correction

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Expose aind-ophys-motion-correction parameters to flexibly motion correct data #25

Closed arielleleon closed 1 month ago

arielleleon commented 3 months ago

This is a requirement for Bergamo data processing but should be developed for broader cases and flexibility so the repo doesn't get written only for Bergamo and Mesoscope data.

User stories (from a user who wants to process 2p planar data):

  1. I want motion correction to process a single HDF5 file.
  2. If the HDF5 data are annotated corresponding to different images from different behavior epochs, I want to specify which frames are used as a reference image and which frames get motion corrected.
  3. I want to specify which frames are used as the reference image and should be able to motion correct all data or specify which frames are motion corrected.
arielleleon commented 3 months ago

Motion correction logic figured out and is being put in place. Notebook in this capsule shows progress. https://codeocean.allenneuraldynamics.org/capsule/8090753/tree?cw=true

Implementation of motion correction logic is being input to feat-single-plane branch.

This should be finished by tomorrow.