Suite2p

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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) […]