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SIMA specifications


Unique identifier OMICS_16271
Alternative name Sequential IMage Analysis
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License GNU General Public License version 2.0
Computer skills Medium
Version 1.3.2
Stability Stable
Maintained Yes




No version available



  • person_outline Patrick Kaifosh

Publication for Sequential IMage Analysis

SIMA citations


Droplet volume variability as a critical factor for accuracy of absolute quantification using droplet digital PCR

Anal Bioanal Chem
PMCID: 5670190
PMID: 28921124
DOI: 10.1007/s00216-017-0625-y

[…] eliminate the possibility of any between-operators effect. For this, images obtained from experimental set-up (1) for day 1 at INRiM were analysed independently by two different operators. All of the sequential image analysis was performed with the automatic droplet measurement protocol, at both NIB and INRiM. […]


Hormonal gain control of a medial preoptic area social reward circuit

Nat Neurosci
PMCID: 5735833
PMID: 28135243
DOI: 10.1038/nn.4487

[…] Following acquisition, data were exported as a tiff series and motion corrected using a planar hidden Markov model (SIMA v1.3;18) and regions of interest (ROIs) were hand drawn around each cell or dendrite on the standard deviation projection tiff image of the motion-corrected video using ImageJ. For chronic imagin […]


Behavioral state modulation of inhibition is context dependent and cell type specific in mouse visual cortex

PMCID: 5030095
PMID: 27552056
DOI: 10.7554/eLife.14985.013

[…] To correct for brain motion after image acquisition, we used 2D plane translation-based image alignment (SIMA 1.2.0, sequential image analysis; ). Regions of interest (ROIs) corresponding to neuronal cell bodies were selected manually by inspecting down-sampled frames (2 Hz), as well as the maximum inten […]


In vivo genetic dissection of tumor growth and the Warburg effect

PMCID: 5030086
PMID: 27585295
DOI: 10.7554/eLife.18126.018
call_split See protocol

[…] eld (Vector Labs, Burlingame, CA). The following antibodies were used: anti-dpERK (1:100; Sigma-Aldrich, St. Louis, MO), anti-phospho Drosophila Akt (Ser505) (1:25; Cell Signaling, Danvers, MA), anti-Sima (1:100; generated by PRF&L, Canadensis, PA), anti-phospho PDH (S293) (1:100; Abcam, Cambridge, MA), anti-PDHK1 (1:100; Abcam), anti-phospho PDHK1 (Tyr243) (1:200; Cell Signaling), anti-phospho JN […]


A conserved polybasic domain mediates plasma membrane targeting of Lgl and its regulation by hypoxia

PMCID: 4621827
PMID: 26483556
DOI: 10.1083/jcb.201503067
call_split See protocol

[…] Fig. S1 shows that hypoxia does not disrupt cell polarity in Drosophila embryonic cells. Fig. S2 shows that inhibition of Lgl PM targeting by hypoxia is modulated by Sima activity but is independent of aPKC/Par-6 complex. Fig. S3 shows that hypoxia reduces intracellular ATP levels to inhibit Lgl PM targeting in Drosophila embryonic epithelial cells and in human MC […]

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SIMA institution(s)
Department of Neuroscience, Columbia University in the City of New York, NY, USA
SIMA funding source(s)
This work was supported by a Howard Hughes Medical Institute International Student Research fellowship, NIH Training Grant T32 GM 7367-38, a Human Frontiers Science Program Grant, a McKnight Foundation Memory and Cognitive Disorders Award, the Brain and Behavior Research Foundation, and NIMH grant 1R01MH100631-01A1.

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