V2.0.0 (2019-04-24) Diocletian

We are pleased to announce the new major release of version SCIPION 2.0. It is freely available for download on Linux here:

http://scipion.i2pc.es/download_form

Key changes for version 2.0 are:

Almost all existing EM packages were updated, such as RELION3, EMAN2.21, Gctf 1.18, SPIDER 25.02, Motioncor2-1.2.1 and others.

Model building tools from CCP4, Chimera, Phenix and powerfit have been added.

Several improvements for streaming: multi-GPU jobs distribution, more protocols supporting batch processing, jobs scheduling, new XMIPP streaming protocols (movie maxshift, ctf selection, GL2D classification on GPU etc.)

Multiple workflow usability and GUI improvements as well as bug fixes for several tasks.

Pluginization: each EM package is now a plugin developed and updated independently from Scipion core. This is a first step towards making Scipion even more modular and easy to use and install for both users and developers. The new repository hosting official plugins is now here:

https://github.com/scipion-em

For your convenience, we have developed a Plugin Manager which provides an easy GUI to manage plugins and associated binaries. We already have over 30 plugins including several new ones, such as 3DFSC, CryoEF, Sphire (crYOLO), EMPIAR depositor and others. For more information on each plugin consult its corresponding repo and/ or developers.

For developers and facility managers, we now have a slack workspace where you can easily reach other developers and facility staff to get quick feedback: https://scipion.slack.com/. Contact us at [email protected] for an invitation.

Installation instructions, pre-requisites and a full list of changes are available on our new documentation website.

v1.2.1

v1.2.1 (2018-10-01) Claudio

Streaming improvements (GPU management, batch processing), New sharpening method, improved monores, bug fixes and more.
See our release notes for more details:
See https://github.com/I2PC/scipion/wiki/Release-Notes#v121-2018-10-01-claudio for more details

v1.2

v1.2 (2018-04-03) Caligula

We have put our efforts in improving the Streaming functionality to work better in facilities. We have also updated some EM packages versions and done some bug-fixing and enhancements.

See https://github.com/I2PC/scipion/wiki/Release-Notes for more details

v1.1

v1.1 (2017-06-14) Balbino

We are very pleased to announce the release of a new version of Scipion. It’s been over a year since the previous and first version and we have been working on 3 main goals for this release:

• Consolidation: We put and will always put our best effort into making Scipion a robust and reliable software. We have improved performance, usability and fixed multiple bugs.
• EM packages integration: We have updated several EM packages to their latest versions (relion 2.0.4) and added new ones (motioncor2, gctf, gautomatch, …). Single movie alignment protocol (as in Scipion 1.0) has been split into several ones for each program.
• Streaming capabilities: To speed up first preprocessing steps we have enabled Scipion to work in “streaming mode”, allowing users to compute aligned movies and estimate CTF as soon as a movie or micrograph comes out of the microscope PC.

See the full release notes here

Please, go to http://scipion.cnb.csic.es/m/download_form to download the bundles and follow our installation guide

v1.0.1

v1.0.1 (2016-06-30)

• Several protocol fixes:
  • Fixed bug when creating the output for Frealign (in some cases some information from input particles was not properly propagated)
  • Fixed some bugs in movie alignment protocols (summovie and unblur) and tests added
  • Some minor bugs fixed in Relion protocols
  • Bugs fixed in Resmap protocol when using two half volumes
• Fixed several bugs in Spider protocols:
  • converting input particles with alignment
  • wrong regular expression for replacing some variables in script template
  • parsing of the resulting dendrogram
  • some additional validations and removed unused code
• Bugfixes and inprovements in Xmipp protocols:
  • Protocols screen-classes merged into one: compare-reprojections
  • Complete refactoring of operate-particles and operate-volumes protocols (previously called 2D and 3D calculator). Tests added
• Picking and Viewer:
  • Warning if particles are picked in a temporary folder and the SetOfParticles was not created
  • Improved implementation of assign-tiltpairs protocol in Xmipp and some refactoring of picking methods
  • Fixed bug that caused GUI to freeze sometimes
  • Some bugs fixed when displaying and exporting particles
  • Sorting arrows displayed after sorting by a column. Hourglass displayed while sorting.
  • Some bug fixed when creating subset from classes
• Other fixes or improvements:
  • ImageHandler's methods convert and writeStack now accepts alignment parameters
  • Fixed bug when displaying Movies summary (sqlite files were not closed)
  • Fixed bug when spawning Eman process to write particles
  • Added REMOTE_MESA_LIB environment var for using OpenGL in remote desktops
  • Created a LegacyProtocol class to read deprecated protocols
  • Cleanup in some tests and added new ones for core classes or functions

v1.0.0

v1.0.0 (2016-02-20) Augusto

• Allows to combine several EM software packages (~ 100 protocols):
  • All protocols from Xmipp
  • Most of protocols from Relion
  • MDA protocols from Spider
  • Some protocols from Eman2/Sparx
  • From Grigorieff lab: CTFFIND, FREALIGN, unblur and summovie.
  • A few tools from Bsoft
  • ResMap, gEMpicker, dogpicker, motioncorr
• Full tracking and reproducibility:
  • Display runs as a list or a tree.
  • Inspect the parameters of a previous run
  • Repeat one or several runs
  • Export/Import a workflow template
• Data analysis:
  • Visualization and operation with Sets. (Particles, Micrographs, CTFs, etc)
  • Visualization of Volumes
  • Resolution and angular distribution plots