Scipion plugin for PYTOM_TM
This plugin provides a wrapper around the program pytom-match-pick (GPU-accelerated template matching for cryo-electron tomography, part of the PyTom suite) to use it within Scipion framework.
Installation
You will need to use 3.0 version of Scipion to run these protocols. To install the plugin, you have two options:
Stable version:
scipion3 installp -p scipion-em-pytom_tmDeveloper’s version
download the repository from github:
git clone -b devel https://github.com/scipion-em/scipion-em-pytom_tm.gitinstall:
scipion3 installp -p /path/to/scipion-em-pytom_tm --devel
To check the installation, simply run the following Scipion test for the plugin:
scipion3 tests pytom_tm.tests.tests_pytom_tm.TestPytomTM
To check the installation, simply run one of the tests. A complete list of tests can be displayed by executing
scipion3 tests --grep pytom_tm --show
Protocols
Template matching : Generates score and angular maps from the introduced tomograms using a reference template and mask, with GPU-accelerated exhaustive angular search.
Extract candidates : Extracts particle coordinates (and orientations) from the score maps produced by template matching with pytom-match-pick.
Latest plugin versions
If you want to check the latest version and release history go to CHANGES
References
Chaillet, M. L., Roet, S., Veltkamp, R. C., & Förster, F. (2025). pytom-match-pick: A tophat-transform constraint for automated classification in template matching. Journal of Structural Biology: X, 11, 100125. https://doi.org/10.1016/j.yjsbx.2025.100125
Chaillet, M. L., van der Schot, G., Gubins, I., Roet, S., Veltkamp, R. C., & Förster, F. (2023). Extensive angular sampling enables the sensitive localization of macromolecules in electron tomograms. International Journal of Molecular Sciences, 24(17), 13375. https://doi.org/10.3390/ijms241713375
1 maintainer
Metadata
1 maintainer
Release files for scipion-em-pytom-tm 3.0.1
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
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| scipion_em_pytom_tm-3.0.1.tar.gz | 49.0 kB | Without provenance | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| scipion_em_pytom_tm-3.0.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 99.1 kB
Release files / scipion_em_pytom_tm-3.0.1.tar.gz
| Download URL | scipion_em_pytom_tm-3.0.1.tar.gz |
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| Size | 49.0 kB |
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Release files / scipion_em_pytom_tm-3.0.1-py3-none-any.whl
| Download URL | scipion_em_pytom_tm-3.0.1-py3-none-any.whl |
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| Size | 50.1 kB |
| Tags | Python 3 |
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