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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




No version available


  • person_outline Keith Typ

Publication for CellSort

CellSort citations


Efficient and accurate extraction of in vivo calcium signals from microendoscopic video data

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

[…] analysis () 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 […]


Automated Functional Analysis of Astrocytes from Chronic Time Lapse Calcium Imaging Data

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

[…] mage 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 a […]


In vivo calcium imaging from dentate granule cells with wide field fluorescence microscopy

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

[…] tiple cells []. This mixed signal can be separated into signal from individual cells using statistical techniques [–]. We used principal and independent component analysis (PCA and ICA)-based method (Cellsort)[] for cell sorting.The mouse was head-fixed on a spherical treadmill that allows the mouse to run freely () []. A custom virtual-reality (VR) system for rodents [–] was used to present spati […]


Rapid signaling in distinct dopaminergic axons during locomotion and reward

PMCID: 4970879
PMID: 27398617
DOI: 10.1038/nature18942

[…] egions 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 a […]

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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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