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Suite2p specifications


Unique identifier OMICS_16272
Name Suite2p
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages MATLAB
License GNU General Public License version 2.0
Computer skills Medium
Stability Stable
Maintained Yes




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  • person_outline Marius Pachitariu

Publication for Suite2p

Suite2p citations


FISSA: A neuropil decontamination toolbox for calcium imaging signals

Sci Rep
PMCID: 5823956
PMID: 29472547
DOI: 10.1038/s41598-018-21640-2

[…] running Ubuntu 17.04 with a six core Intel Core i7-6800 K [email protected] GHz). FISSA is thus well suited for processing large datasets with long imaging periods. However, as opposed to other methods (cNMF, suite2P), FISSA does not automatically segment the images into defined ROIs; therefore, the total time for data processing also depends on the method used for defining ROIs as well as on the data load […]


Life Long Genetic and Functional Access to Neural Circuits Using Self Inactivating Rabies Virus

PMCID: 5509544
PMID: 28689641
DOI: 10.1016/j.cell.2017.06.014

[…] the power at sample was controlled in the range 30-40 mW. Data analysis was performed in ImageJ and MATLAB and was restricted to cell bodies. Detection of region of interest (ROI) was performed with Suite2p (). The relative changes in fluorescence were calculated as dF/F0 = (F(t)-F0)/(F0). Orientation tuning curves were generated by taking the mean response for each orientation during the entire […]


Two photon calcium imaging of the medial prefrontal cortex and hippocampus without cortical invasion

PMCID: 5643091
PMID: 28945191
DOI: 10.7554/eLife.26839.026
call_split See protocol

[…] urface. This might explain why the number of detected circles increased as the imaging depth increased to 1000 µm ().Motion correction for calcium imaging was performed by phase-correlation using the Suite2P package (, After the motion correction, images were three frame-averaged before being analyzed. A constrained non-negative matrix factorization (cNMF) al […]

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Suite2p institution(s)
UCL Institute of Neurology, London, UK; UCL Department of Neuroscience, Physiology, and Pharmacology, London, UK; Gatsby Computational Neuroscience Unit, London, UK; UCL Institute of Ophthalmology, London, UK
Suite2p funding source(s)
This work was supported by the Wellcome Trust (95668, 95669, 108726), the Simons Foundation (325512), by a four-year Gatsby Foundation PhD studentship, by Marie Skłodowska-Curie Fellowships and by a four-year Wellcome Trust PhD studentship in Neuroscience.

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