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PyTom specifications

Information


Unique identifier OMICS_15665
Name PyTom
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.971
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Friedrich Förster <>

Publication for PyTom

PyTom in publications

 (6)
PMCID: 5815350
PMID: 29311144
DOI: 10.1523/JNEUROSCI.1548-17.2017

[…] microscopy data bank accession code emd-5224; ), after low-pass filtering and scaling to the same pixel size as the tomograms, was used as the template to localize ribosomes in the synapses using pytom (). the template structures were then placed in the final segmentation using ucsf chimera. svs were identified as described below and rendered based on their size. the receptor-like structures […]

PMCID: 5508204
PMID: 28695917
DOI: 10.1038/ncomms15957

[…] generate an initial model that is essentially a donut-shaped structure. it was then used as a template to automatically identify particles from 23 tomograms by using template matching implemented in pytom. a total of 18,400 ring-like structures (128 × 128 × 64 pixels) were extracted for subtomogram analysis by using tomographic package i3 (ref. ). two distinct class averages emerged […]

PMCID: 5516000
PMID: 28781998
DOI: 10.1007/s41048-017-0040-0

[…] more accessible with the surge of open-access software for spt, such as av3 (förster and hegerl ), peet (nicastro et al. ) (available through imod (kremer et al. )), jsubtomo (huiskonen et al. ), pytom (hrabe et al. ), dynamo (castaño-díez et al. ), eman2 (galaz et al. ; murray et al. ; galaz-montoya et al. ), and relion (bharat et al. )., the evolution of cryoet can be followed […]

PMCID: 5321747
PMID: 28218252
DOI: 10.1038/ncomms14516

[…] motion in electron micrographs acquired with the k2 direct electron detector. phase reversals resulting from the contrast transfer function were corrected in single projections with matlab and pytom using strip-based periodogram averaging. interactively located gold markers were used for tilt series alignment, and tomograms were reconstructed in pytom by weighted back projection (binned […]

PMCID: 4598622
PMID: 26411746
DOI: 10.1038/ncomms9403

[…] a quasi-expectation maximization protocol implemented in the matlab toolbox av3 (ref. ). correction of phase reversals due to the contrast transfer function was performed using matlab scripts and pytom on single projections by strip-based periodogram averaging. tilt series were aligned with the help of interactively located gold markers and tomograms (object pixel: 2.1 nm) were reconstructed […]


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PyTom institution(s)
Max-Planck Institute of Biochemistry, Martinsried, Germany
PyTom funding source(s)
This work has been funded by a Career Development Award from the Human Frontier Science Projects (HFSP).

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