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tomotwin-cryoet

cryo-ET particle picking by representation and metric learning

https://github.com/mpi-dortmund/tomotwin-cryoet

Science Score: 62.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 4 committers (50.0%) from academic institutions
  • ✓
    Institutional organization owner
    Organization mpi-dortmund has institutional domain (www.mpi-dortmund.mpg.de)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (4.7%) to scientific vocabulary

Keywords

cryo-em cryo-et deep-learning metric-learning particle-picking
Last synced: 9 months ago · JSON representation ·

Repository

cryo-ET particle picking by representation and metric learning

Basic Info
  • Host: GitHub
  • Owner: MPI-Dortmund
  • License: mpl-2.0
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 64.3 MB
Statistics
  • Stars: 36
  • Watchers: 7
  • Forks: 8
  • Open Issues: 6
  • Releases: 12
Topics
cryo-em cryo-et deep-learning metric-learning particle-picking
Created about 4 years ago · Last pushed 10 months ago
Metadata Files
Readme License Citation

README.md

CodeFactor codecov

TomoTwin

Particle picking in Tomograms using triplet networks and metric learning

TomoTwin Logo TomoTwin Logo

Instructions

For installation instructions and tutorials please see our documentation

Owner

  • Name: Max Planck Institute of Molecular Physiology
  • Login: MPI-Dortmund
  • Kind: organization
  • Location: Dortmund, Germany

Citation (CITATION.cff) 

cff-version: 1.2.0
title: TomoTwin
message: "If you want to cite this repository, please use the metadata from this file."
type: software
authors:
  - given-names: Gavin
    family-names: Rice
    email: gavin.rice@mpi-dortmund.mpg.de
    orcid: 'https://orcid.org/0000-0002-7151-5904'
  - given-names: Thorsten
    family-names: Wagner
    email: thorsten.wagner@mpi-dortmund.mpg.de
    orcid: 'https://orcid.org/0000-0002-1550-8275'
  - given-names: Markus
    family-names: Stabrin
    email: markus.stabrin@mpi-dortmund.mpg.de
    orcid: 'https://orcid.org/0000-0003-0191-6419'
  - given-names: Daniel
    family-names: Prumbaum
    email: daniel.prumbaum@mpi-dortmund.mpg.de
  - given-names: Stefan
    family-names: Raunser
    email: stefan.raunser@mpi-dortmund.mpg.de
    orcid: 'https://orcid.org/0000-0001-9373-3016'
identifiers:
  - type: doi
    value: 10.1038/s41592-023-01878-z
    description: TomoTwin publication
  - type: doi
    value: 10.1101/2022.06.24.497279
    description: TomoTwin Preprint
  - type: doi
    description: This is the collection of archived snapshots of all versions of TomoTwin
    value: 10.5281/zenodo.7956443
repository-code: 'https://github.com/MPI-Dortmund/tomotwin-cryoet'
url: 'https://cryolo.readthedocs.io/en/stable/'
abstract: "cryo-ET particle picking using triplet networks and metric learning."
keywords:
  - cryo-em
  - cryo-et
  - metric-learning
  - deep learning
  - picking
license: MPL-2.0

GitHub Events

Total
  • Create event: 13
  • Release event: 1
  • Issues event: 22
  • Watch event: 5
  • Delete event: 12
  • Issue comment event: 16
  • Push event: 77
  • Pull request review event: 1
  • Pull request event: 20
  • Fork event: 2
Last Year
  • Create event: 13
  • Release event: 1
  • Issues event: 22
  • Watch event: 5
  • Delete event: 12
  • Issue comment event: 16
  • Push event: 77
  • Pull request review event: 1
  • Pull request event: 20
  • Fork event: 2

Committers

Last synced: about 3 years ago

All Time
  • Total Commits: 332
  • Total Committers: 4
  • Avg Commits per committer: 83.0
  • Development Distribution Score (DDS): 0.184
Top Committers
Name Email Commits
thorsten.wagner t****r@m****e 271
thorstenwagner t****1@p****e 53
Gavin Rice g****e@m****e 6
Gavin 6****1@u****m 2
Committer Domains (Top 20 + Academic)
mpi-dortmund.mpg.de: 2 posteo.de: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 53
  • Total pull requests: 88
  • Average time to close issues: 3 months
  • Average time to close pull requests: 4 days
  • Total issue authors: 23
  • Total pull request authors: 4
  • Average comments per issue: 3.49
  • Average comments per pull request: 0.56
  • Merged pull requests: 84
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 14
  • Pull requests: 25
  • Average time to close issues: 5 months
  • Average time to close pull requests: 1 day
  • Issue authors: 10
  • Pull request authors: 3
  • Average comments per issue: 1.79
  • Average comments per pull request: 0.12
  • Merged pull requests: 23
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • thorstenwagner (17)
  • kimdn (5)
  • azazellochg (5)
  • jychoi0616 (3)
  • alisterburt (2)
  • dahui-y (2)
  • hamid13r (2)
  • JachyLikeCoding (2)
  • Dendooventom (2)
  • pankajumich (1)
  • ashishsdalvi (1)
  • odespard (1)
  • kephale (1)
  • NoahHenrikKleinschmidt (1)
  • bionanopatterning (1)
Pull Request Authors
  • thorstenwagner (66)
  • YousefMetwally (16)
  • GavinR1 (10)
  • kephale (2)
Top Labels
Issue Labels
enhancement (8) maintenance (4) bug (2) documentation (2) good first issue (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 124 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 37
  • Total maintainers: 1
pypi.org: tomotwin-cryoet

Picking procedure for cryo em tomography

  • Versions: 37
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 124 Last month
Rankings
Dependent packages count: 6.6%
Stargazers count: 16.6%
Downloads: 17.0%
Average: 20.3%
Forks count: 30.5%
Dependent repos count: 30.6%
Maintainers (1)
sphire-devel
Last synced: 10 months ago

Dependencies

docs/requirements.txt pypi
  • docutils <0.18
  • sphinx-prompt ==1.3.0
setup.py pypi
  • mrcfile *
  • numba *
  • numpy *
  • pandas *
  • pystardb ==0.3.1
  • pytorch-metric-learning *
  • scikit-image *
  • scikit-learn *
  • setuptools_scm *
  • tabulate *
  • tensorboard *
  • tqdm *
.github/workflows/checks_tests_deploy.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • codecov/codecov-action v3 composite
  • conda-incubator/setup-miniconda v2 composite
  • jlumbroso/free-disk-space main composite