PALMsiever statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PALMsiever

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PALMsiever specifications


Unique identifier OMICS_06522
Name PALMsiever
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


No version available



  • person_outline Thomas Pengo

Publication for PALMsiever

PALMsiever citations


A peptide tag specific nanobody enables high quality labeling for dSTORM imaging

Nat Commun
PMCID: 5834503
PMID: 29500346
DOI: 10.1038/s41467-018-03191-2

[…] Imaging and post-processing of BC2TLC3B cells was done as described in the “dSTORM imaging and post-processing” section. The obtained localization files were loaded into the MatLab-based software PALMsiever. Density-based clustering analysis was performed with the density-based spatial clustering of applications with noise (DBSCAN) algorithm (DBSCAN parameters: ε = 50 nm; MinPts = 40). Three c […]


Functional mapping of brain synapses by the enriching activity marker SynaptoZip

Nat Commun
PMCID: 5663910
PMID: 29089485
DOI: 10.1038/s41467-017-01335-4

[…] emoving the initial baseline (no SB in the bath). For super-resolution localization of SB uptake in synaptic vesicles, we used a GSD microscope (SR GSD 3D, Leica Microsystems, Buffalo Grove, IL), the PALMsiever Matlab toolbox was then used to generate images from localization lists (kernel density estimation, pixel size set to 4.12 nm). Standard Matlab functions were utilized for circle segmentati […]


Defined chromosome structure in the genome reduced bacterium Mycoplasma pneumoniae

Nat Commun
PMCID: 5344976
PMID: 28272414
DOI: 10.1038/ncomms14665

[…] microscope (Leica, Wetzlar, Germany) using the proprietary Leica software, equipped with a 1.46 NA 100 × TIRF objective and an Andor iXon EMCCD camera. We processed the data using rapidSTORM and used PALMsiever for filtering and rendering. Finally, using Fiji, the distances were calculated between the centre of mass of the observed probes.Additional images were taken on a Nikon N-STORM system in d […]

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PALMsiever institution(s)
Design of Biological Systems, Systems Biology, Center for Genomic Regulation, Barcelona, Spain; Advanced Light Microscopy Unit, Center for Genomic Regulation, Barcelona, Spain; Laboratory for Experimental Biophysics, Institute for Physics of Biological Systems, School of Basic Sciences, Swiss Federal School of Technology, Lausanne, Switzerland

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