Fix motion correction and CNMF for 3D movies #300
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rebase this on main once #298 is merged |
ethanbb
changed the title
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wait until next release of caiman and then pin the next release of mescore to that |
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Caiman PR is merged, but still waiting for next release to mark as ready for review. |
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Caiman 1.11.2 is released |
kushalkolar
requested changes
Aug 11, 2024
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Lgtm! |
kushalkolar
approved these changes
Aug 22, 2024
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The mcorr algorithm currently fails when run on a 3D movie during correlation image calculation. This is due to some code in caiman that could probably also be changed to get it to work (flatironinstitute/CaImAn#1363 does half of it), but this PR should fix mcorr in a way that is also compatible with existing caiman versions:
load_file_chaindoes not get called, which meansis3Dis not needed (otherwise this throws an error).This PR is dependent on #298 (to avoid an ugly merge) so I'm submitting it as a draft for now. Also, it would be good to add a test case for 3D motion correction (with test data and everything). But at least the current tests pass (except for the 2 that are always failing) so it doesn't break 2D mcorr.