LBM-Suite2p-Python Documentation

LBM-Suite2p-Python Documentation#

See the suite2p documentation for more details.

Documentation Contents#

Helpful Suite2p Issues#

Issue

Topic

Summary

#921

Registration Artifacts

Try smaller block_size and larger spatial_taper to reduce wobbliness caused by black background inclusion in registration.

#880

Running on a Cluster

Discussion on running Suite2p on a cluster.

#851

ROI Overlap

ROIs will overlap if signals overlap, but if an ROI overlaps more than ops['max_overlap'], it gets discarded. Set ops['max_overlap'] = 1 to keep all ROIs. ops['allow_overlap'] = 0 (default) ignores overlapping pixels when computing signals.

#837

ROI Binning

tau determines data binning before ROI detection: Bin size = ops['tau'] * ops['fs']. More binning helps with noisy data. ROI Detection Overview.

#787

Thresholding

ops['threshold_scaling'] affects dim regions.

#690

Channel Registration

Discussion on registering one channel to another.

#627

Fluorescence & Neuropil Signals

Explanation of F (Fluorescence) and Fneu (Neuropil Fluorescence) in Suite2p output.

#758

Running on a Cluster

More discussion on looping over databases (dbs) when running Suite2p on a cluster.

References#

This pipeline uses several core tools for calcium imaging processing and analysis.

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Contents