This is a dynamic list of methods grouped by package that are present in Scipion. Some of them might come from a development environment and soon will be released.
Plugin url https://github.com/scipion-em/scipion-em-appion.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-aretomo.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-atomstructutils.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-atsas.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-bamfordlab.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-bsoft.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-ccp4.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-chimera.
Available in Linux. Scientific software, Image processing, cryo emThis plugin allows to use chimeraX commands within the Scipion framework.
Plugin url https://github.com/scipion-em/scipion-em-chimera.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-cistem.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-continuousflex.
Available in Linux. Scientific software, Image processing, cryo emThis plugin provide a wrapper around Cryoassess software tools for automatic micrograph and 2D classes assessment.
Plugin url https://github.com/scipion-em/scipion-em-cryoassess/.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-cryocare.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-cryodrgn.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-cryoef.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/mcgill-femr/scipion-em-cryomethods.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-cryosparc2.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-deepfinder.
Available in Linux. Scientific software, Image processing, cryo emscipion-ed-dials is the Scipion-ED plugin to use programs from DIALS for Electron Diffraction image processing.
Plugin url https://github.com/scipion-ed/scipion-ed-dials.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-dynamo.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-eman2.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-emantomo.
Available in Linux. Scientific software, Image processing, cryo emThis plugin allows to use different utils for cryo-EM facilities (like monitors) within the Scipion framework.
Plugin url https://github.com/scipion-em/scipion-em-facilities.
Available in Linux. Scientific software, Image processing, cryo emThis project is a Scipion plugin to make depositions to https://www.ebi.ac.uk/pdbe/emdb/empiar
Plugin url https://github.com/scipion-em/scipion-em-empiar.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-emxlib.
Available in Linux. Scientific software, Image processing, cryo emISPyB monitor for facility ESRF
Plugin url https://github.com/scipion-em/scipion-em-esrf.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-fsc3d.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-gautomatch.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-gctf.
Available in Linux. Scientific software, Image processing, cryo emDEPRECATED! Plugin to use Grigorieff Lab (not CisTEM) programs within the Scipion framework.
Plugin url https://github.com/scipion-em/scipion-em-grigoriefflab.
Available in Linux. Scientific software, Image processing, cryo emThis plugin includes two protocols to provide wrappers around Multivariate Statistical Analysis (MSA) module of IMAGIC software suite
Plugin url https://github.com/scipion-em/scipion-em-imagic.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-imod.
Available in Linux. Scientific software, Image processing, cryo emMethods that are currently in development
Available in Linux. Scientific software, Image processing, cryo emISPyB monitor for scipion
Plugin url https://github.com/scipion-em/scipion-em-ispyb.
Available in Linux. Scientific software, Image processing, cryo emA "bag" for protocols that has been deprecated
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-localrec.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-locscale.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-motioncorr.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-novactf.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-phenix.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/cossorzano/scipion-pkpd.
Available in Linux. Scientific software, Image processing, cryo emProgram from Alexandre Bonvin and Gydo van Zundert (Utrecht University) for rigid body fitting of an atomic structure into a 3D volume
Plugin url https://github.com/scipion-em/scipion-em-powerfit.
Available in Linux. Scientific software, Image processing, cryo emThis plugin provide a wrapper around ProDy software: A Python Package for Protein Dynamics Analysis
Plugin url https://github.com/scipion-em/scipion-em-prody.
Available in Linux. Scientific software, Image processing, cryo emscipion-ed is the base plugin defining the Domain for Electron Diffraction image processing
Plugin url https://github.com/scipion-ed/scipion-ed.
Available in Linux. Scientific software, Image processing, cryo emBase plugin to deal with EM data. Provides all the import protocols and the model for EM objects (Micrograpths, Movies, Volumes, etc)
Plugin url https://github.com/scipion-em/scipion-em.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-pyseg.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-relion.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-reliontomo.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-resmap.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-sidesplitter.
Available in Linux. Scientific software, Image processing, cryo emThis plugin allows to use Simple programs within the Scipion framework.
Plugin url https://github.com/scipion-em/scipion-em-simple.git@python3_migration.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-sphire.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-spider.
Available in Linux. Scientific software, Image processing, cryo emThis plugin provides wrappers for Susan software: subtomogram averaging (StA) workflow for CryoET based on sub-stacks of images instead of sub-volumes of tomograms.
Plugin url https://github.com/scipion-em/scipion-em-susantomo.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-tomo.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-tomo3d.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-tomoj.
Available in Linux. Scientific software, Image processing, cryo emScipion plugin for segmentation and annotation of membranes in tomograms (with TomoSegmenTV and memb-annotator, respectively)
Plugin url https://github.com/scipion-em/scipion-em-tomosegmemtv.
Available in Linux. Scientific software, Image processing, cryo emThis plugin provides a wrapper for TomoTwin software: Particle picking in Tomograms using triplet networks and metric learning
Plugin url https://github.com/scipion-em/scipion-em-tomotwin.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-tomoviz.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/scipion-em/scipion-em-topaz.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/I2PC/scipion-em-xmipp2.git.
Available in Linux. Scientific software, Image processing, cryo emPlugin to use Xmipp programs within the Scipion framework.
Plugin url https://github.com/i2pc/scipion-em-xmipp.
Available in Linux. Scientific software, Image processing, cryo emPlugin url https://github.com/i2pc/scipion-em-xmipptomo.
Available in Linux. Scientific software, Image processing, cryo em