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iSMS specifications


Unique identifier OMICS_29558
Name iSMS
Alternative name Single-Molecule FRET Microscopy Software
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages MATLAB
Computer skills Advanced
Version 2.01
Stability Stable
Maintained Yes




No version available


  • person_outline Victoria Birkedal
  • person_outline Daniel Gudnason

Additional information

Publication for iSMS

iSMS citations


Real time observation of conformational switching in single conjugated polymer chains

Sci Adv
PMCID: 5817931
PMID: 29487904
DOI: 10.1126/sciadv.aao5786

[…] ovies in o-DCB (514 single chains). For sample TES-P3HT-L, we collected 18 movies in DMSO (231 single chains) and 10 movies in o-DCB (764 single chains). The raw data were analyzed using the software iSMS () and custom-built Matlab algorithms to extract the single-chain intensity traces. Each intensity peak in the raw movies was fitted to a 2D Gaussian function. Next, the volume of the correspondi […]


Optical Voltage Sensing Using DNA Origami

PMCID: 5851876
PMID: 29430924
DOI: 10.1021/acs.nanolett.7b05354

[…] The raw data acquired from the single-molecule fluorescence recordings were visualized and processed using iSMS (v.2.01), an open-source software package for wide-field, single-molecule FRET microscopy on immobilized molecules. […]


Molecular mechanisms of Bdp1 in TFIIIB assembly and RNA polymerase III transcription initiation

Nat Commun
PMCID: 5526994
PMID: 28743884
DOI: 10.1038/s41467-017-00126-1

[…] r IXon Ultra 897, EM-gain 20, framerate 40 Hz, 400 frames) in a dual-view configuration (TripleSplit, Cairn Research) was used to record both detection channels.The videos were analyzed employing the iSMS software using the programs’ default settings. Molecule spots were detected using a threshold of 100 for ATTO532 and ATTO647N spots. FRET efficiencies were calculated as proximity ratios from flu […]


Tailored protein encapsulation into a DNA host using geometrically organized supramolecular interactions

Nat Commun
PMCID: 5316895
PMID: 28205515
DOI: 10.1038/ncomms14472

[…] , glucose oxidase (Sigma-Aldrich, 0.92 mg ml−1), catalase (Sigma-Aldrich, 0.04 mg ml−1) and β-D-(+) glucose (Sigma-Aldrich, 4.5 mg ml−1). Data analysis was performed by the home-made software package iSMS. […]


A direct view of the complex multi pathway folding of telomeric G quadruplexes

Nucleic Acids Res
PMCID: 5159523
PMID: 27799468
DOI: 10.1093/nar/gkw1010

[…] ted onto the EMCCD camera (Andor, iXON 3) by a wedge mirror. Movies were recorded with a 200 ms integration time per frame with a total length of 600 s (10 min) and were analyzed using the home-built iSMS software (). Only the trajectories with single-step donor and/or acceptor photobleaching, or showing clear anti-correlated donor–acceptor dynamics, were selected for further analysis. The FRET ef […]


Single molecule imaging of non equilibrium molecular ensembles on the millisecond timescale

Nat Methods
PMCID: 4814340
PMID: 26878382
DOI: 10.1038/nmeth.3769

[…] previously described. State assignment (, right panel) is performed using SKM. Although several other Markov modeling utilities are available and could be used for this purpose (HaMMy, vbFRET, SMART, iSMS, TwoTone), SKM is much faster and this facilitates analysis of the large datasets associated with sCMOS. […]

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iSMS institution(s)
Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark; Centre for DNA Nanotechnology (CDNA), Aarhus University, Aarhus, Denmark
iSMS funding source(s)
Supported by grants from the Danish National Research Foundation to the CDNA Center (grant number DNRF81), from the Danish Council for Independent Research’s carrier program Sapere Aude and from Aarhus University Research Foundation.

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