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cortex-lab / Suite2P

Tools for processing 2P recordings
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neuropil subtraction with small ROIs #119

Closed ransona closed 6 years ago

ransona commented 6 years ago

Hi Thanks for developing this brilliant pipeline. I'm experiencing a bug with extracting rois from bouton data that specifically comes up when I set db(i).diameter < 5. It seems to be related to the neuropil extraction or subtraction as if I get it with ops0.signalExtraction = 'surround' but not with 'raw' or 'regression'. It throws the following error:

715 total ROIs, err 0.4588, thresh 0.0190 1190 total ROIs, err 0.4512, thresh 0.0190 1363 total ROIs, err 0.4483, thresh 0.0190 1415 total ROIs, err 0.4474, thresh 0.0190 1415 total ROIs, err 257248016.0000, thresh 0.0190 1415 total ROIs, err 256747776.0000, thresh 0.0190 1415 total ROIs, err 256708928.0000, thresh 0.0190 Error using bsxfun Non-singleton dimensions of the two input arrays must match each other.

Error in svdecon (line 36) V = bsxfun(@(x,c)x./c, V, s');

Error in extractSignalsSurroundNeuropil2 (line 95) [u, s, v] = svdecon(ratCS);

Error in run_pipeline (line 78) [ops, stat, Fcell, FcellNeu] = extractSignalsSurroundNeuropil2(ops, stat);

Error in master_file_AR1 (line 83) run_pipeline(db, ops0);

36 V = bsxfun(@(x,c)x./c, V, s');

Thanks Adam

carsen-stringer commented 6 years ago

sorry this code is actually our "automatic" drift detection (it computes the ratio between the inner pixels of the cell and the outer pixels - if they change non-uniformly then it suggests drift). I think your boutons are too small for this to work, I've added an option to shut this off (by default it's off). The option is ops.getZdrift.

ransona commented 6 years ago

ah I see, thanks for sorting it!

On Mon, Jun 4, 2018 at 4:02 PM, carsen-stringer notifications@github.com wrote:

sorry this code is actually our "automatic" drift detection (it computes the ratio between the inner pixels of the cell and the outer pixels - if they change non-uniformly then it suggests drift). I think your boutons are too small for this to work, I've added an option to shut this off (by default it's off). The option is ops.getZdrift.

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