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--- sphire_1_4 [2021/02/15 14:34]
fschoenfeld
+++ sphire_1_4 [2021/07/08 12:01]
mstabrin [Documentation & Tutorial]
@@ Line 24: / Line 24: @@
     * multiple improvements for better results.
-==== Documentation & Tutorial ====
+===== Documentation & Tutorial =====
   * Find the [[http://sphire.mpg.de/wiki/doku.php|SPHIRE documentation]] here.
-  * Find the [[ftp://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.)
+  * 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 installer uses Anaconda, which should install independently of the choice of Linux distribution.  The Mac installer is experimental.
-Here are the downloads for Mac and Linux:
+===== 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 (Expermential)]]
+  * [[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
+SPHIRE does not support Windows.
 </note>
-These external tools will be needed to run all tools in SPHIRE:
-  * [[https://cryolo.readthedocs.io/en/latest/|crYOLO download]]
-  * [[http://sphire.mpg.de/wiki/doku.php?id=auto_2d_class_selection|Cinderella download]]
-  * Unblur ships with [[https://cistem.org/|cisTEM]]
-  * [[gpu_isac|GPU ISAC]]
 <note tip>
 **TranSPHIRE for automatated preprocessing**
-Furthermore, we recommend to use TranSPHIRE for automated preprocessing: [[https://github.com/MPI-Dortmund/transphire|TranSPHIRE GitHub page]]
+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 =====
-==== Installation instructions ====
 Find the installation instructions here:

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