Xmipp

Release Notes

Current version: 3.0

Version 3.1

Release date: 8-4-2014

  • Protocol for using Relion with Xmipp added.
  • RANSAC protocol implemented for initial volume estimation.
  • Protocols to import/export using the EMX formats.
  • Protocol to study continuous heterogeneity through Normal Mode Analysis
  • Manual and supervised picking steps have been merged.
  • Many other useful protocols:
    • Merge sets of particles
    • Create a subset of particles
    • Compare classes to a volume (screen classes)
    • Denoise a set of experimental images using a set of classes (denoise particles)
    • Random Conical Tilt revised
    • Conversion from PDB
    • Initial volume through simulated annealing
    • Analysis of the residuals of a set of images
    • Create mask for a volume
    • Preprocess volumes
    • Resolution 3D
    • Align volume
    • Estimate helical parameters
    • Compute SAXS curves
    • CLTomo for subtomogram averaging
    • Soft X-rays tomography: Import, fast align, reconstruct
    • Metadata split and utilities
    • Image calculator
    • Particle quality assessment and sorting
  • References to articles added to each protocol in the summary.
  • Several bugs have been fixed from version 3.0.

Version 3.0

Release date: 26-3-2013

  • Changes in core C++ libraries
    • Image related classes have been re-factored allowing to read most of the image formats used in the field.
    • Adopted a subset of STAR text files as input/output format (internal implementation using sqlite of a MetaData class)
    • Complete refactor of programs, now the input is defined better (invalid command line is validated before proceed, etc)
    • More tools for further developments of parallel (MPI and threads) programs.
  • Project and Protocols
    • The project is more structured and organized.
    • Protocol parameters definition have been improved (conditional params and more validation)
    • Easier way to configure launching jobs and further monitoring.
  • Visualization
    • Java development of metadata visualization (for both table and gallery view)
    • Image display is connected with ImageJ, allowing integration.
    • Particle picking was re-written from scratch using Java Swing/ImageJ.
    • Implementation of a customized file explorer for EM-related files.

Version 2.3

Release date: 13-4-2009
  • Bug fixes: 2.2-bug1

Version 2.2

Release date: 8-10-2008
  • Bug fixes: 2.0.2-bug1

Version 2.0.2

Release date: 11-1-2008
  • Bug fixes: 2.0.1-bug1, 2.0.1-bug2, 2.0-bug3

Version 2.0.1

Release date: 13-12-2007
  • Bug fixes: 2.0-bug1, 2.0-bug2

Version 2.0

Release date: 29-11-2007
  • Added standardized protocols with graphical interface
  • Added MLF2D and MLF3D classification
  • Made CTF-estimation more robust

Version 1.1

Release date:11-1-2007
  • Added ML3D classification
  • Added compilation using Scons
  • Added binaries distribution for i386 and a64