pytom-match-pick: A tophat-transform constraint for automated classification in template matching pubmed.ncbi.nlm.nih.gov/40475324/ #cryoem

Automated detection of macromolecules in cryo-ET data of cellular samples is challenging. Here, we introduce "pytom-match-pick", a GPU-accelerated, open-source interface that improves the efficiency and accuracy of macromolecule detection in cellular contexts: www.sciencedirect.com/science/arti...

Nice! Was picking with the standalone pytom-match-pick?

1/3 Our template matching package has changed name to pytom-match-pick (github.com/SBC-Utrecht/...) as it started diverging from the original project! It is now also on pypi, so you can easily install it with pip (thanks to twitterless sroet!)

Using the amazing #pytom-match-pick we guide you through particle picking. From the template matching results we show you how to perform STA in #RELION5 pushing Ribosomes to their absolute limit (Nyquist)!
3 /🧵

Thanks Marten! With pytom-match-pick, getting the ribosome average ready for the rendering was a breeze! :)

New Title Alert: pytom-match-pick- a GPU accelerated python module to significantly improve the speed and sensitivity using template matching to detect macromolecules from tomograms.

Learn more here: https://buff.ly/4f5JkBl

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Yes indeed! This is the only time i went "out" of RELION for this test. pytom-match-pick has been working very well for my targets, and directly outputs RELION5 compatible coordinate files.

Warptools has an inbuilt aretomo3 wrapper that you can use. If your plan is to use M, i recommend preprocessing the data with warptools. Pytom-match pick natively supports warptools xml files for on the fly filter calculation.

Thanks Marten! pytom-match-pick was extremely helpful here 😉

Technical Notes: This month's software push includes updates to BioEmu, BoltzGen, ChimeraX, DOCK, Google Cloud SDK, HADDOCK3, NAMD, OpenFold, ORCA, pytom-match-pick, pyTME, SamTOOLS, Schrödinger 2025-3 and 2025-4, and Topaz.

More information here: buff.ly/lgtNHCd

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Confirmed by gold-standard FSC of course :)
pytom-match-pick does not use projections unlike RELION5 and I suppose there is also quite the difference from the previous pseudo-subtomos

Technical Notes: May's software push includes updates to AlphaFold3, autoPROC, BoltzGen, Buster, CCP4, ChemEx, COOT, cryoCAT , DIALS, Maxit, MotionCor3, OpenFreeEnergy, OpenMM, PowerFit, pytom-match-pick, TOMOMAN, Topaz, Volume_Seg_Tool, and Warp.

More here: buff.ly/xcoDMki

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August's software push includes - AlphaFold3, AlphaPulldown, AmberTools, CCP4, Chromap, COOT, cryoDRGN, DIALS, Foldtree, ICM Browser, NMRFx-Anaylst, OpenFold3, Open Force Field Toolkit, OpenMM, pyCoAn, pytom-match-pick, RDKit, Scipion, Schrödinger, Warp, and XDS.

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June's software push includes updates to BioEmu, BLAST+, Boltz-1, ChimeraX, ColabFold, Cryo_fit, cryosparc-tools, Durin, Dynamo, GROMACS, LocScale, Modeller, NAMD, PowerFit, PyEM, Pytom-match-pick, QFit, SAMtools, Scipion, Topaz, & Vesicle-Picker.

More information here: buff.ly/2BmKW9G

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September's software push includes updates to- AlphaPulldown, Boltz, ChemEM, ColabDesign, cryoDRGN, EMReady2, GROMACS, HADDOCK, NMRFxAnalyst, NMRFxStructure, PowerFit, PyTom-Match-Pick, R, RDKit, RFDiffusion, Scipion, SSDraw, Starparser, Topaz, Volume_Seg_Tool, & Warp.

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Technical Notes: October's software push includes updates to ChimeraX, DeepRank-GNN-ESM, MDAnalysis, NGLView, NmrPipe, Open Force Field Toolkit, Open Free Energy, PowerFit, PyTOM-match-pick, RDKit, and TomoNet.

More here: buff.ly/uLpQznY

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pytom-match-pick: a tophat-transform constraint for automated classification in template matching https://www.biorxiv.org/content/10.1101/2024.09.17.613497v1