Suite2p specifications

Information


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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Maintainer


  • person_outline Marius Pachitariu <>

Publication for Suite2p

Suite2p in publications

 (5)
PMCID: 5946730
PMID: 29656873
DOI: 10.1016/j.neuron.2018.03.037

[…] and others (n = 7) in the acallosal binocular zone (abz, 15-30°). we observed no difference in results between recordings in monocular and binocular zones ()., raw calcium movies were analyzed with suite2p, which performs several processing stages (). first, suite2p registers the movies to account for brain motion, then clusters neighboring pixels with similar time courses into regions […]

PMCID: 5871355
PMID: 29469809
DOI: 10.7554/eLife.28728.031

[…] similar results with related methods that use a similar low-rank matrix factorization model (e.g. diego-andilla and hamprecht, 2013, or maruyama et al., 2014). we also tried the similar model in suite2p (pachitariu et.al., 2016), which projects the background onto a prespecified spatial basis, and again found that this led to worse results in recovering the background signal in the datasets […]

PMCID: 5662625
PMID: 29084948
DOI: 10.1038/s41467-017-01371-0

[…] of initial 10 frames) and all the other frames (typically 1–2 × 104 frames). a semi-automatic segmentation of regions of interest (rois) was then performed in the motion-corrected data using the suite2p toolbox (https://github.com/cortex-lab/suite2p). a neuropil region was also determined automatically for each roi as a surrounding region (2–8 μm from each roi) that does not include the soma […]

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 […]

PMCID: 5643091
PMID: 28945191
DOI: 10.7554/eLife.26839.026

[…] 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 (, http://github.com/cortex-lab/suite2p). after the motion correction, images were three frame-averaged before being analyzed. a constrained non-negative matrix factorization (cnmf) […]


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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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