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DeconSTORM specifications


Unique identifier OMICS_28424
Name DeconSTORM
Alternative name Deconvolution-stochastic optical reconstruction microscopy
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes




No version available



  • person_outline Xiaowei Zhuang
  • person_outline Eran Mukamel

Publication for Deconvolution-stochastic optical reconstruction microscopy

DeconSTORM citations


Multiple signal classification algorithm for super resolution fluorescence microscopy

Nat Commun
PMCID: 5155148
PMID: 27934858
DOI: 10.1038/ncomms13752

[…] sparsity of blinking, density of emitters, number of frames, excitation power and chemical environment. Further comparison of MUSICAL with other statistical super-resolution techniques, such as SOFI, deconSTORM, 3B and ESI indicates competitive and often superior performance of MUSICAL. Here, we mention that MUSICAL performs better than SOFI and ESI in terms of resolution and image quality, howeve […]


Bayesian localization microscopy based on intensity distribution of fluorophores

PMCID: 4348249
PMID: 25672498
DOI: 10.1007/s13238-015-0133-9

[…] use a fluorophore to emit light: transferring from emitting to emitting and transferring from not emitting to emitting. For convenience, we only considered two states: emitting and not emitting. Like deconSTORM (Mukamel et al., ), we assigned an exponential prior distribution to parameter, γk(x), which represents the estimated intensity at location x in frame k. γk(x) is based on a weighted averag […]


Spatial Covariance Reconstructive (SCORE) Super Resolution Fluorescence Microscopy

PLoS One
PMCID: 4005777
PMID: 24788039
DOI: 10.1371/journal.pone.0094807

[…] istributed bright emitters, Holden et al. used a software package from astronomy research to separate closely located Gaussians in a technique called DAOSTORM . Compressed sensing STORM (CSSTORM) and deconSTORM also address the overlapping PSF problem and are able to work with slightly a overlapping density of active emitters , . Higher emitter density still remains challenging for these essential […]


Super Resolution Imaging Strategies for Cell Biologists Using a Spinning Disk Microscope

PLoS One
PMCID: 3793996
PMID: 24130668
DOI: 10.1371/journal.pone.0074604

[…] py: 90×90 pixels 5000 frames (). 3B and QuickPALM image analysis was carried out using the FiJi plugin , . RainSTORM image analysis was carried out in Matlab, ( FasterSTORM and DeconSTORM analysis were carried out according to published instructions. The Localizer suite of super-resolution image analysis algorithms was used to conduct SOFI and GLRT image analysis. For th […]


Test Samples for Optimizing STORM Super Resolution Microscopy

PMCID: 3857894
PMID: 24056752
DOI: 10.3791/50579

[…] rainSTORM 27, rapidSTORM 24,25 , palm3d 12 and QuickPALM 26software. If the raw data contains a lot of overlapping signals then algorithms which may be more appropriate include DAOSTORM 34, 3B 35 and deconSTORM 36. Moreover, these algorithms contain thresholds for various criteria such as signal counts, or photons per blink, as well as various different image display options such as visualizing wi […]


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DeconSTORM institution(s)
Center for Brain Science, Harvard University, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Department of Physics, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
DeconSTORM funding source(s)
Supported by a Swartz Fellowship in Theoretical Neuroscience, and by the National Institutes of Health and Gatsby Charitable Foundation.

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