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@emdb-empiar EMDB and EMPIAR

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    31 repositories

    • added_annotations

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Feb 18, 2026Feb 18, 2026

    • emdb-chart-builder

      Public
      EMDB Chart Builder - A standalone charting tool for visualizing EMDB and EMPIAR archive data"
      JavaScript
      •
      Apache License 2.0
      •0•0•0•0•Updated Dec 8, 2025Dec 8, 2025

    • emdb-schemas

      Public
      A collection of emdb.xsd schemas
      Python
      •0•0•0•0•Updated Nov 17, 2025Nov 17, 2025

    • emdb-api-wrapper

      Public
      EMDB API wrapper class
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Oct 15, 2025Oct 15, 2025

    • pubmed-author-affiliations

      Public
      Search PubMed for author affiliations of EMDB associated publications
      searchdoipubmedauthorship-analysisemdb
      Python
      •
      Other
      •1•1•0•0•Updated Aug 4, 2025Aug 4, 2025

    • empiar-depositor

      Public
      Python package for depositing into EMPIAR
      Python
      •
      Apache License 2.0
      •4•7•1•1•Updated Apr 7, 2025Apr 7, 2025

    • json_to_mmcif

      Public
      Converting JSON to mmCIF, as well as adding to and modifying an mmCIF file using a JSON file.
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Mar 28, 2025Mar 28, 2025

    • EMharvest

      Public
      DM
      •
      BSD 3-Clause "New" or "Revised" License
      •3•0•0•0•Updated Mar 28, 2025Mar 28, 2025

    • emdb-xml-translator

      Public
      A set of translators for converting EMDB XML files 1.9 <-> 3.0 <-> 1.9
      Python
      •0•2•0•0•Updated Jan 21, 2025Jan 21, 2025

    • noid

      Public
      Mint NOIDs using a CLI or API
      Python
      •3•5•0•0•Updated Aug 31, 2024Aug 31, 2024

    • emdb-json-schemas

      Public
      JSON Schemas for files describing the EMDB archive
      1•0•0•0•Updated Jul 10, 2024Jul 10, 2024

    • emdb-molstar

      Public
      Molstar EMDB implementation
      TypeScript
      •
      Apache License 2.0
      •36•0•0•0•Updated Jun 4, 2024Jun 4, 2024

    • SPW

      Public
      EMPIAR Sample Preparation Collection Schema
      0•2•1•0•Updated May 2, 2024May 2, 2024

    • sfftk

      Public
      Toolkit for working with EMDB-SFF and other segmentation file formats
      Python
      •
      Apache License 2.0
      •3•5•0•0•Updated Feb 26, 2024Feb 26, 2024

    • bandbox

      Public
      bandbox is a CLI tool to quickly evaluate how organised your dataset is.
      Python
      •
      Apache License 2.0
      •0•2•0•0•Updated Jan 2, 2024Jan 2, 2024

    • sfftk-plus

      Public
      Extended toolkit for working with EMDB-SFF and OMERO (using VTK for geometrical manipulation)
      Python
      •
      Apache License 2.0
      •0•1•0•0•Updated Nov 29, 2023Nov 29, 2023

    • styled

      Public
      Style your terminal with ease!
      Python
      •
      Apache License 2.0
      •0•0•1•0•Updated Oct 26, 2023Oct 26, 2023

    • masks

      Public
      simple tool to create image masks
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Oct 20, 2023Oct 20, 2023

    • sfftk-rw

      Public
      Toolkit for reading and writing EMDB-SFF files
      Python
      •
      Apache License 2.0
      •0•2•0•0•Updated Oct 3, 2023Oct 3, 2023

    • maptools

      Public
      Python
      •0•0•0•0•Updated Mar 16, 2023Mar 16, 2023

    • emdb-empiar.github.io

      Public
      Repository documentation for EMDB/EMPIAR software projects
      HTML
      •
      Apache License 2.0
      •0•2•0•0•Updated Jan 30, 2023Jan 30, 2023

    • EMDB-SFF

      Public
      Open data model for segmentation file format
      HTML
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 30, 2023Jan 30, 2023

    • ahds

      Public
      Python package to parse and provide access to headers and data streams in Amira(R) files
      Python
      •
      Apache License 2.0
      •2•8•0•0•Updated Oct 4, 2022Oct 4, 2022

    • sfftk-migrate

      Public
      Utility to Update Old EMDB-SFF Files
      Python
      •
      Apache License 2.0
      •0•0•1•0•Updated Aug 3, 2022Aug 3, 2022

    • meshmaker

      Public
      VTK-based program to compute isosurfaces from CCP4 maps
      C++
      •
      Apache License 2.0
      •1•0•0•0•Updated Jun 15, 2022Jun 15, 2022

    • 3dstrudel

      Public
      Base library of the 3D-STRUDEL project
      Python
      •
      Apache License 2.0
      •0•3•1•0•Updated Dec 24, 2021Dec 24, 2021

    • strudel_score

      Public
      Python
      •0•0•0•0•Updated Nov 15, 2021Nov 15, 2021

    • names

      Public
      Key utilities designed to abstract the names of entries in EMDB, EMPIAR and the upcoming segmentation (image annotation) archive.
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Sep 23, 2021Sep 23, 2021

    • EMDBassist

      Public
      Python
      •1•0•0•0•Updated Feb 26, 2021Feb 26, 2021

    • cif-emdb-translator

      Public
      Translator for mmCIF files to XML header files that comply with EMDB version 3 and later schemas
      Python
      •0•0•0•0•Updated May 12, 2020May 12, 2020