Repositories list

• scipion-em-bsoft

  Public
  Plugin to use Bsoft programs within the Scipion framework

  spa

  Python

  •

  GNU General Public License v3.0

  •0•2•2•0•Updated Dec 9, 2025Dec 9, 2025

• scipion-pyworkflow

  Public
  Underlying pyworkflow module for the Scipion framework

  core

  Python

  •

  GNU General Public License v3.0

  •8•5•40•2•Updated Dec 9, 2025Dec 9, 2025

• scipion-em-roodmus

  Public
  atom

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 9, 2025Dec 9, 2025

• scipion-em-reweighting

  Public
  scipion plugin for ensemble reweighting

  Python

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Dec 8, 2025Dec 8, 2025

• scipion-em-facilities

  Public
  Plugin for Cryo-EM facilities to be used within Scipion framework

  other

  Python

  •

  GNU General Public License v3.0

  •1•0•6•2•Updated Dec 5, 2025Dec 5, 2025

• scipion-em-relion

  Public
  Plugin to use Relion SPA programs within the Scipion framework

  spa

  Python

  •

  GNU General Public License v3.0

  •0•3•27•5•Updated Dec 5, 2025Dec 5, 2025

• scipion-em-dynamo

  Public
  Dynamo tomography plugin for Scipion

  tomo

  Python

  •

  GNU General Public License v3.0

  •0•1•5•1•Updated Dec 5, 2025Dec 5, 2025

• scipion-em-reliontomo

  Public
  Plugin to use Relion tomography programs within the Scipion framework

  tomo

  Python

  •

  GNU General Public License v3.0

  •3•2•5•1•Updated Dec 4, 2025Dec 4, 2025

• scipion-em-emantomo

  Public
  Plugin to use Eman2 tomography programs within the Scipion framework

  tomo

  Python

  •

  GNU General Public License v3.0

  •0•2•7•0•Updated Dec 4, 2025Dec 4, 2025

• scipion-em-opusdsd

  Public
  Plugin to use OPUS-DSD programs within the Scipion framework

  spa

  Python

  •

  GNU General Public License v3.0

  •0•3•0•0•Updated Dec 4, 2025Dec 4, 2025

• scipion-em-tomo

  Public
  Base tomography Scipion plugin with data model definition

  tomo

  Python

  •

  GNU General Public License v3.0

  •5•9•42•1•Updated Dec 4, 2025Dec 4, 2025

• scipion-em-imod

  Public
  Plugin to use some of the Tomography tools from IMOD in Scipion

  tomo

  Python

  •

  GNU General Public License v3.0

  •2•2•19•3•Updated Dec 3, 2025Dec 3, 2025

• scipion-em-warp

  Public
  Plugin to use Warp programs within the Scipion framework

  spatomo

  Python

  •

  GNU General Public License v3.0

  •0•0•1•1•Updated Dec 3, 2025Dec 3, 2025

• scipion-em-novactf

  Public
  Plugin to use NovaCTF in scipion

  tomo

  Python

  •

  GNU General Public License v3.0

  •0•1•1•2•Updated Dec 2, 2025Dec 2, 2025

• scipion-em-bindcraft

  Public
  Scipion plugin to design proteins using BindCraft (pipeline based on AlphaFold2 backpropagation, MPNN, and PyRosetta )

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 27, 2025Nov 27, 2025

• scipion-em-carbonara

  Public
  Scipion plugin that allows to run CARBonAra, a deep learning method for samplings sequences based on structure atomic coordinates

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 27, 2025Nov 27, 2025

• scipion-em

  Public
  Base Scipion plugin defining objects and protocols for EM

  spacoretomo

  Python

  •

  GNU General Public License v3.0

  •7•9•22•7•Updated Nov 25, 2025Nov 25, 2025

• scipion-em-modelangelo

  Public
  Scipion plugin for ModelAngelo: an automatic atomic model building program for cryo-EM maps. With or without providing a sequence.

  scienceworkflowimage-processing+ 4scientific-computingfaircryoemscipion

  Python

  •

  GNU General Public License v3.0

  •0•1•0•1•Updated Nov 25, 2025Nov 25, 2025

• scipion-em-kiharalab

  Public
  Utilities from Kihara Lab

  scipionkiharalab

  Python

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Nov 24, 2025Nov 24, 2025

• docs

  Public
  Scipion documentation repository

  other

  Python

  •

  GNU General Public License v3.0

  •6•1•2•0•Updated Nov 24, 2025Nov 24, 2025

• scipion-em-smartscope

  Public
  Plugin to manage the interaction with the SmartScope framework.

  Python

  •

  GNU General Public License v3.0

  •0•4•1•1•Updated Nov 20, 2025Nov 20, 2025

• scipion-em-topaz

  Public
  Scipion plugin to integrate Topaz particle picker

  spa

  Python

  •

  GNU General Public License v3.0

  •0•0•3•0•Updated Nov 18, 2025Nov 18, 2025

• scipion-em-cryocare

  Public
  Plugin to integrate cryoCARE: denoiser for tomography

  tomo

  Python

  •

  GNU General Public License v3.0

  •0•3•0•1•Updated Nov 17, 2025Nov 17, 2025

• scipion-em-tomosegmemtv

  Public
  Scipion plugin for segmentation and annotation of membranes (with tomoSegmenTV and membSegAnnotator)

  tomo

  Python

  •

  GNU General Public License v3.0

  •0•4•2•1•Updated Nov 14, 2025Nov 14, 2025

• scipion-em-tomo3d

  Public
  Plugin for the software of Jose Jesus Fernandez

  tomo

  Python

  •

  GNU General Public License v3.0

  •0•0•2•1•Updated Nov 14, 2025Nov 14, 2025

• scipion-em-cistem

  Public
  Plugin to use cisTEM programs within the Scipion framework

  spatomo

  Python

  •

  GNU General Public License v3.0

  •4•1•1•0•Updated Nov 14, 2025Nov 14, 2025

• scipion-em-gapstop

  Public
  Plugin to use Gapstop_TM in Scipion

  tomo

  Python

  •

  GNU General Public License v3.0

  •0•0•0•1•Updated Nov 14, 2025Nov 14, 2025

• scipion-em-aretomo

  Public
  Plugin to use AreTomo within the Scipion framework

  tomo

  Python

  •

  GNU General Public License v3.0

  •0•1•1•1•Updated Nov 14, 2025Nov 14, 2025

• scipion-em-deepfinder

  Public
  Scipion plugin for deepfinder (tomography picker)

  tomo

  Python

  •

  GNU General Public License v3.0

  •0•3•2•1•Updated Nov 14, 2025Nov 14, 2025

• scipion-em-fidder

  Public
  tomo

  Python

  •

  GNU General Public License v3.0

  •0•0•0•1•Updated Nov 14, 2025Nov 14, 2025