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CellSort specifications


Unique identifier OMICS_14374
Name CellSort
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Keith Typ <>

Publication for CellSort

CellSort in publications

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

[…] () and the original cnmf method ()., after choosing the thresholds for seed pixels (), we run cnmf-e in full automatic mode, without any manual interventions. two open-source matlab packages, cellsort (https://github.com/mukamel-lab/cellsort; ) and ca_source_extraction (https://github.com/epnev/ca_source_extraction; ), were used to perform pca/ica () and basic cnmf (), respectively. since […]

PMCID: 5509822
PMID: 28769780
DOI: 10.3389/fninf.2017.00048

[…] analysis has so far made any effort to tackle the problems caused by the propagation phenomena. to validate the necessity of explicitly modeling the propagation phenomena, we compared fasp with “cellsort” (mukamel et al., ), one of the most popular ca2+ dynamic detection algorithms that work quite well on neuronal ca2+ imaging data. ignoring the effect of propagation, cellsort makes a basic […]

PMCID: 5507494
PMID: 28700611
DOI: 10.1371/journal.pone.0180452

[…] turboreg []. we used an averaged image of the entire frames as a reference for image alignment. spatial filters corresponding to individual cells were identified using a pca and ica-based algorithm (cellsort 1.0) (mukamel et al., 2009)., ca2+ activity was extracted by applying the spatial filters to the time-lapse image. the ca2+ transients were identified by searching each trace for local […]

PMCID: 4970879
PMID: 27398617
DOI: 10.1038/nature18942

[…] of the field) from the mean fluorescence image for each time series. fluorescence traces and rois from putative single axon segments from the sparsely labeled fields (, –) were generated using cellsort with the following parameters: smoothing width = 1.5, mu = 0.8, principal components = 200, area limits = 50 – 3000 pixels. roi fluorescence traces and roi morphology were visibly inspected […]

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CellSort institution(s)
Chemical & Biological Engineering, Northwestern University, Evanston, USA
CellSort funding source(s)
This work was supported by the Bill and Melinda Gates Foundation [OPP1061177], a Howard Hughes Medical Institute Gilliam Fellowship, and NIH training grant [T32-GM008449-23].

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