cryoem

There are 4 repositories under cryoem topic.

• tbepler / topaz

  Pipeline for particle picking in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Also featuring micrograph and tomogram denoising with DNNs.

  cryoemparticle-pickingmachine-learningcnnpositive-unlabeledobject-detectionpytorchtopaztopaz-denoisedenoisingcryo-emtopaz-em
  Language:Jupyter Notebook 169
• awesome-cryoem

  kuixu / awesome-cryoem

  A collaborative list of awesome CryoEM (Cryo Electron Microscopy) resources.

  cryo-emelectron-microscopydensity-map3d-reconstruction3d-denoisemodel-buildingprotein-structurestomographycryoem
  133

• phonchi / Computational-CryoEM

  A curated list of awesome computational cryo-EM methods.

  cryo-emelectron-microscopysingle-particle-analisyscomputational-biologystructural-biologycryoem
  Language:Jupyter Notebook 92

• jewettaij / superpose3d

  register 3D point clouds using rotation, translation, and scale transformations.

  3dcryo-emcryoempoint-cloudpoint-cloud-registrationregistrationrmsdscale-transformationsstructure-comparison
  Language:Python 40
• xmipp

  I2PC / xmipp

  Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy.

  cryo-emcryoemscipion
  Language:C++ 38
• privateer

  glycojones / privateer

  The Swiss Army knife for carbohydrate structure validation, refinement and analysis

  crystallographycryoemcarbohydratesglycosylationvalidationrefinementccp4ccp-emccp4i2clippersnfgsvgyork
  Language:C++ 26
• TomoBEAR

  KudryashevLab / TomoBEAR

  TomoBEAR is a configurable and customizable modular pipeline for streamlined processing of cryo-electron tomographic data for subtomogram averaging.

  cryo-emcryoemcryo-etcryoetprocessingpipelinestructural-biologyparallelcluster-computingparallel-computingclustertememettomographyreconstructionautomatedalignmentparticle-pickingtemplate-matching
  Language:MATLAB 26

• IsoNet-cryoET / spIsoNet

  Overcoming the preferred orientation problem in cryoEM with self-supervised deep-learning

  cryo-emcryoemdeep-learningimage-processing
  Language:Python 16

• DaisukeMiyamoto / aws-parallelcluster-relion

  example set up for Relion on AWS ParallelCluster for CryoEM

  aws-parallelclustercryo-emcryoemrelion
  Language:Shell 12

• nysbc / appion-protomo

  A Docker-based distribution of Appion-Protomo.

  tomographycryoetcryoemprotomoalignment
  Language:PHP 11
• mrc-em-gnome-thumbnailer

  the-lay / mrc-em-gnome-thumbnailer

  .MRC and .EM thumbnailer for GNOME

  thumbnailsthumbnailergnomegnome-desktopcryoemcryoet
  Language:Python 7

• Guillawme / angdist

  Plot the 2D histogram of Euler angles covered by a set of cryo-EM particles

  visualizationplothistogramcryo-emrelioncryoemorientationseuler-angles
  Language:Python 6

• jewettaij / visfd

  volumetric image toolkit for simple feature detection (segment tomograms)

  3d-imagescryo-emcryoemelectron-microscopyimage-processingmembrane-detectionmrc-formatsegmentationtensor-votingtomography
  Language:C++ 6

• ShkolniskyLab / kltpicker

  KLT picker: Particle picking using data-driven optimal templates (Python version)

  particle-pickingelectron-microscopycryoem
  Language:Python 6

• Guillawme / localres

  Plot the histogram of local resolution values of a cryo-EM reconstruction

  cryo-emcryoemcryosparchistogramlocal-resolutionplotrelionresolutionvisualizvisualization
  Language:Python 4

• PlethoraChutney / exawatcher

  A lightweight script to monitor RELION jobs and send information over Slack DMs

  cryoemrelion
  Language:Python 4

• Guillawme / classconvergence

  Plot the class distribution as a function of iteration from a Class2D or Class3D job from RELION

  cryo-emcryoemvisualizationrelionclassification
  Language:Python 3

• Guillawme / countparticles

  Report the number of particles in each class from a run_data.star file produced by RELION

  cryoemclassdistributionvisualizationrelionplotcryo-em
  Language:Python 3

• rajanprabu / cryoem-scripts

  helper scripts for Electron microscopy data processing

  cryoemelectron-microscopyememanimodrelion
  Language:Python 3

• hbhargava7 / cryoem-data-simulation

  Python3 tools for simulating cryoEM particle data.

  cryoem-data-simulationsimulated-particlescryoemstructural-biologybiophysics
  Language:Jupyter Notebook 2

• vigo332 / cryosparc_onthefly

  A simple script to run CryoSparc cluster on the fly inside a SLURM HPC job

  cryosparcslurmcryoem
  Language:Shell 2

• fmi-basel / RosEM

  Pipeline and GUI for cryoEM model refinement using Rosetta and Phenix

  cryoemrefinementrosettaphenixguimodelling
  Language:Python 1

• phonchi / Cryo-forum

  A Framework for Orientation Recovery with Uncertainty Measurement in Cryo-EM Image Analysis

  computational-biologycryo-emcryoemimage-processingneural-networkuncertainty-quantificationpose-estimationsingle-particle-analisys
  Language:Jupyter Notebook 1

• scipion-em / scipion-em-modelangelo

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

  cryoemfairimage-processingsciencescientific-computingscipionworkflow
  Language:Python 1

• bioinsilico / EM_FILTER

  Keras scripts

  cryoemconvolutional-neural-networksmicrographfilter
  Language:Python 0
• riboxyz

  rtviii / riboxyz

  cryoemhidden-markov-modelmmcifpdbribosomestructural-biologytypes
  Language:C 0

• ShkolniskyLab / kltpicker_matlab

  KLT picker: Particle picking using data-driven optimal templates (MATLAB version)

  particle-pickingelectron-microscopycryoem
  Language:MATLAB 0

• CERIT-SC / scipion-docker

  Scipion (Cryo em image processing framework (https://scipion.i2pc.es/)) adapted to run in Kubernetes.

  cryo-emcryoemcudadesktopkubernetesscipionvnc
  Language:Python

• CERIT-SC / scipion-portal

  Web Portal for deploying Scipion-in-K8S instances (https://github.com/CERIT-SC/scipion-docker)

  cryo-emcryoemkubernetesscipionweb-portal
  Language:JavaScript

• Guillawme / topaztrainmetrics

  Plot metrics from a Topaz training run

  cryo-emcryoemtopazparticle-pickingvisualization
  Language:Python