====== SPHIRE 1.4 / EMAN 2.9 ======

We are happy to announce the release of **SPHIRE 1.4**!

This release adds GUI support for GPU ISAC and makes SPHIRE fully compatible with [[https://transphire.readthedocs.io/|TranSPHIRE]], allowing you to [[https://www.nature.com/articles/s41467-020-19513-2|create on-the-fly reconstructions during data acquisition]].

As usual, this release is a combined release of [[https://sphire.mpg.de/wiki/doku.php?id=start|SPHIRE]], [[https://blake.bcm.edu/emanwiki/EMAN2|EMAN2]], and [[http://sparx-em.org/sparxwiki/Introduction|SPARX]].

===== What's new =====

The key additions to the [[http://sphire.mpg.de/|SPHIRE]] package in this update include:

  * **SPHIRE:** The GUI now allows easy access to the SPHIRE [[pipeline:subtract:start|signal subtraction pipeline]] to be used after 3D refinement.
  * **SPHIRE:** Easy access to mFSC (mask-independent, local resolution capable FSC) via the SPHIRE GUI ([[https://doi.org/10.1107/S2052252520011574|mFSC developed by Pawel Penczek]]).
  * **SPHIRE:** [[gpu_isac|GPU ISAC]] can now be linked with and used from the SPHIRE GUI.

  * **AutoSPHIRE:** Further improved processing of helical data in Helical Mode.
  * **AutoSPHIRE:** Fully compatible and ready to be used with [[https://transphire.readthedocs.io/|TranSPHIRE]] to on-the-fly create initial reconstructions during data acquisition.

  * **SPHIRE internal:** SPHIRE has been ported to Python 3.
  * **SPHIRE internal:** A wide range of internal changes, including:
    * multiple optimizations for improved runtime,
    * multiple bug fixes for increased stability,
    * multiple improvements for better results.

===== Documentation & Tutorial =====

  * Find the [[http://sphire.mpg.de/wiki/doku.php|SPHIRE documentation]] here.
  * Find the [[https://ftp.gwdg.de/pub/misc/sphire/sphire_1_3_tutorial/sphire_1_3.pdf|SPHIRE tutorial (direct link to .pdf file)]] here. (The SPHIRE tutorial is a step-by-step walkthrough of processing a data set from beginning to end, including pre-processed data milestones.)


===== Download =====

The SPHIRE installer uses Anaconda, which installs independently of your choice of Linux distribution.

  * [[https://cryoem.bcm.edu/cryoem/static/software/release-2.9/eman2.9_sphire1.4_sparx.linux64.sh| Linux installer]]
  * [[https://cryoem.bcm.edu/cryoem/static/software/release-2.9/eman2.9_sphire1.4_sparx.MacOS.sh| Mac installer (experimental)]]

Find our additional SPHIRE tools here:

  * **crYOLO** for picking ([[https://cryolo.readthedocs.io/en/latest/|download]]).
  * **Cinderella** for 2D class selection ([[http://sphire.mpg.de/wiki/doku.php?id=auto_2d_class_selection|download]]).
  * **GPU ISAC** for 2D clustering ([[https://sphire.mpg.de/wiki/doku.php?id=gpu_isac|download]]).
  * **Unblur** ships with ([[https://cistem.org/|cisTEM]]).

<note warning>
SPHIRE does not support Windows.
</note>

<note tip>
**TranSPHIRE for automatated preprocessing**

You can use TranSPHIRE to automate the cryo-EM pre-processing pipeline. When combined with AutoSPHIRE, you can also use TranSPHIRE to produce on-the-fly reconstructions during data acquisition ([[https://github.com/MPI-Dortmund/transphire|GitHub]], [[https://transphire.readthedocs.io/|documentation]]).
</note>

===== Installation instructions =====

Find the installation instructions here:

  * [[https://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstallAnaconda/2.9|SPHIRE binary installation instructions]] 
  * [[https://blake.bcm.edu/emanwiki/EMAN2/COMPILE_EMAN2_ANACONDA|SPHIRE source code installation instructions]] 

Older and newer versions:
  * [[https://blake.bcm.edu/emanwiki/EMAN2/Install|Installation instructions versions]]