===== SPHIRE Wiki =====

If you want to dig deep into the SPHIRE pipeline then you are in the right place. This Wiki will provide you with information about the major programs within SPHIRE and how to use them. Of course, you will also find information about installation, additional utilities, frequently asked questions and known issues. In addition, you can find usage tutorials and SPHIRE's version history. Just follow the links in the sidebar.

Happy cryo-EM'ing!

===== Short application info =====

| \\ **Projects** \\  \\ Main project settings, such as name, pixel, and particles sizes.|{{  :icons:icon_settings_64.png?nolink&64x64}}|
| \\ **Cter** \\  \\ CTF estimation and graphical evaluation tool.|{{  :icons:icon_ctf_64.png?nolink&64x64}}|
| \\ **Window** \\  \\ Particle picking and extraction.|{{  :icons:icon_window_few_64.png?nolink&64x64}}|
| \\ **ISAC** \\  \\ Reproducible class average calculation.|{{  :icons:icon_isac_plus_few_64.png?nolink&64x64}}|
| \\ **Viper** \\  \\ Reproducible //ab initio// model calculation.|{{  :icons:icon_viper6_darkerlines_64.png?nolink&64x64}}|
| \\ **Meridien** \\  \\ Automatic high-resolution 3D refinement.|{{  :icons:icon_meridien_darkerline_64.png?nolink&64x64}}|
| \\ **Sort3D** \\  \\ Reproducible 3D clustering.|{{  :icons:icon_sort3d_64.png?nolink&64x64}}|
| \\ **Subtract** \\  \\ Signal subtraction.|{{  :icon_subtract_64.png?nolink&64x64}}|
| \\ **LocalRes** \\  \\ Real-space local resolution calculation.|{{  :icons:icon_localres_64.png?nolink&64x64}}|
| \\ **Movie** \\  \\ Movie frame alignment with [[http://grigoriefflab.janelia.org/unblur|Unblur]] and drift evaluation tools.|{{  :icons:icon_movie_64.png?nolink&64x64}}|
| \\ **Utilities** \\  \\ Tools and scripts to make your life easier.|{{  :icons:icon_utilities2_64.png?nolink&64x64}}|

|