Release notes

Release 3.20.07 -

• Fast CTF estimation
• CTF includes phase shifts now
• Selection of alpha helices or beta sheets from a PDB (xmipp_pdb_select)
• Centering a PDB (xmipp_pdb_center)
• New Protocol: MicrographCleaner is a new algorithm that removes coordinates picked from carbon edges, aggregations, ice crystals and other contaminations
• New functionality: The protocol compare reprojections can now compute the residuals after alignment
• New protocol: Split frames divide input movies into odd and even movies so that they can be processed independently
• New protocol: Continuous heterogeneity analysis using spherical harmonics (not ready to be used)
• Bug fixing when some micrograph has no coordinates in the consensus-picking.
• New functionalities: Different architectures and training modes
• Normal Mode Analysis protocols have been moved to the plugin ContinuousFlex
• Fixing MPI version of the Fourier Reconstruction
• New protocol: local CTF integration and consensus protocol for local ctf (also the viewers)
• Local CTF analysis tools: Not yet ready for general public
• New functionallity: Introducing the posibility of automatic estimation of the gain orientation.
• Bugs fixings regarding stability on streaming processing
• Support of heterogeneous movie sets
• New protocol: Clustering of subtomogram coordinates into connected components that can be processed independently
• New Protocol: Removing duplicated coordinates
• New protocol: Subtomograms can be projected in several ways to 2D images so that 2D clustering tools can be used
• New protocol: Regions of Interest can be defined in tomograms (e.g., membranes)
• Bug fixing in mask3d protocol
• Bug fix: in helical search symmetry protocol
• Enhanced precision of the FlexAlign program
• Now, deepLearningToolkit is under its own conda environment
• Multiple protocols accelerated using GPU
• New functionality: Xmipp CTF estimation can now take a previous defocus and do not change it
• New functionallity: CTF-consensus is able to take the primary main values or an average of the two.
• New functionallity: CTF-consensus is able to append metadata from the secondary input
• New functionality: Xmipp Highres can now work with non-phase flipped images
• New functionality: Xmipp Preprocess particles can now phase flip the images
• New protocol: Tool to evaluate the quality of a map-model fitting
• Allowing multi-GPU processing using FlexAlign
• Improvement in monores and localdeblur
• Randomize phases also available for images
• Change the plugin to the new Scipion structure
• Migrating the code to python3

Release 3.19.04

• New protocols:

  • New protocol: 3D bionotes
  • New protocol: Align volume and particles
  • New protocol: Center particles
  • New protocols: GL2D, GL2D streaming and GL2D static
  • New protocol: 2D kmeans clustering
  • New protocol: compare angles
  • New protocol: consensus 3D classes
  • New protocol: CTF consensus
  • New protocol: deep denoising
  • New protocols: Eliminate empty particles and eliminate empty classes
  • New protocol: Extract unit cell
  • New protocol: Generate reprojections
  • New protocol: metaprotocol heterogenety output, metaprotocol heterogeneity subset and metaprotocol heterogeneity
  • New protocol: Movie Max Shift
  • New protocol: particle boxsize
  • New protocol: pick noise
  • New protocol: significant heterogeneity
  • New protocol: swarm consensus intial volumes
  • New protocol: directional ResDir
  • New protocol: local monoTomo
  • New protocol: deep consensus picking
  • New protocol: screen deep learning
  • New protocol: split volume hierarchical
  • New protocol: trigger data

• New features:

  • Highres can now take a global alignment performed by any other method
  • A short presentation with some of the new algorithms can be seen here.

• New code structure:

This release is the first one after a big re-factorization of the code in several repositories. The previous Xmipp version was inside the Scipion's repository. However, we have now splited the code in 4 Xmipp repositories:

• Xmipp Core: This repository contains the most basic software for cryo-EM (coded in C++), such us multidimensional matrices, image definition, Fast Fourier Transform, metadata management, symmetry groups, Xmipp programs...
• Xmipp Software: This repository contains image processing methods for cryo-EM, data management... (mostly coded in C++)
• Xmipp Viz: This repository contains visualizations programs for cryo-EM data, such us Movies, Micrographs, Particles, Coordinates, stack of images... (coded in java).
• Xmipp plugin: This is the plugin to be installed in Scipion.