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flatironinstitute / CaImAn

Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.
https://caiman.readthedocs.io
GNU General Public License v2.0
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cell is sliding and how can I exclude it? #1180

Closed zhouyi0812 closed 10 months ago

zhouyi0812 commented 1 year ago

Hello! I encounter a problem that a few of my cells are sliding in widefield and the rest is fixed. And the package identify the whole trajectory as a footprint. I tried to adjust the gsig and gsiz to exclude but seems doesn't work. I wonder if there is anyway improve it by which parameter? Thank you!

5_Original_and_Accepted_Components_098C1d16_B2_C1_1_00d00h00m

EricThomson commented 1 year ago

This is a problem with motion correction not source extraction. If you have movement like this, it will be a problem.

zhouyi0812 commented 1 year ago

Thank you! I tried to limited the max_shifts for the movie, however I think it just doesn't work for that and still identify the object. So I wonder before I decide to toss the movie, if it is possible that I just deleted the specific ROI in the result? and if this will impact the traces from other cells?

EricThomson commented 1 year ago

You can delete specific ROIs, but also you could run motion correction again with a smaller patch width to try to mop up residual motion.