pytom-match-pick 0.4.3

PyTOM's GPU template matching module as an independent package

GPU template matching for cryo-ET

GPU template matching, originally developed in PyTom, as a standalone python package that can be run from the command line.

Requires

miniconda3
nvidia-cuda-toolkit

Installation

There are 2 options for creating a conda environment. We recommend option (1) which will later allow cupy to build against a system installed cuda-toolkit. Compared to option (2) this can give an almost two-fold speedup:

1. (recommended) Create a new python 3 environment:

   conda create -n pytom_tm python=3
   

2. Create a new environment with a prebuild cupy version and complete CUDA-toolkit. This is more reliable, but takes more disk space and has less optimal performance.

   conda create -n pytom_tm -c conda-forge python=3 cupy cuda-version=11.8
   

Once the environment is created, activate it:

conda activate pytom_tm

Then clone the repository and install it with pip (building cupy can take a while!):

git clone https://github.com/SBC-Utrecht/pytom-match-pick.git
cd pytom-match-pick
python -m pip install '.[plotting]'

The installation above also adds the optional dependencies [matplotlib, seaborn] which are required to run pytom_estimate_roc.py. They are not essential to the core template matching functionality, so for some systems (such as certain cluster environments) it might be desirable to skip them. In that case remove [plotting] from the pip install command:

python -m pip install .

Tests

To run the unittests:

cd tests
python -m unittest discover

If cupy is not correctly installed, this should raise some errors:

python -c "import cupy as cp; a = cp.zeros((100,100))"

To solve cupy installation issues, please check the cupy docs. It might be solved by installing a specific build compatible with the installed cuda toolkit.

Usage

Detailed usage instructions are available on the wiki: https://github.com/SBC-Utrecht/pytom-match-pick/wiki

Also, a tutorial can be found on the same wiki: https://github.com/SBC-Utrecht/pytom-match-pick/wiki/Tutorial

The following scripts are available to run with --help to see parameters:

• create a template from an mrc file containing a density map: pytom_create_template.py --help
• create a mask for template matching: pytom_create_mask.py --help
• run template matching with the mask (.mrc) and template (.mrc) on a tomogram (.mrc): pytom_match_template.py --help
• extract candidates from a job file (.json) created in the template matching output folder: pytom_extract_candidate.py --help
• estimate an ROC curve from a job file (.json): pytom_estimate_roc.py --help
• merge multiple star files to a single starfile: pytom_merge_stars.py --help

Contributing

Contributions to the project are very welcome! Feel free to make a pull request or suggest an implementation in the issues. For PR's we will gladly give you feedback on how to integrate the code.

Citation

For a reference on GPU accelerated template matching in tomograms please see the IJMS publication.

@Article{ijms241713375,
    AUTHOR = {Chaillet, Marten L. and van der Schot, Gijs and Gubins, Ilja and Roet, Sander and Veltkamp, Remco C. and Förster, Friedrich},
    TITLE = {Extensive Angular Sampling Enables the Sensitive Localization of Macromolecules in Electron Tomograms},
    JOURNAL = {International Journal of Molecular Sciences},
    VOLUME = {24},
    YEAR = {2023},
    NUMBER = {17},
    ARTICLE-NUMBER = {13375},
    URL = {https://www.mdpi.com/1422-0067/24/17/13375},
    ISSN = {1422-0067},
    DOI = {10.3390/ijms241713375}
}