===== 2DX Workshop 2016 =====

**The fifth edition of our hands-on workshop on "2D Electron Crystallography"**

The hand-on workshop on the processing of images from cryo-electron microscopy of 2D crystals of membrane proteins (electron crystallography) will provide the theoretical background and practical applications in advanced image processing algorithms. The workshop will use the 2dx software system and will feature theoretical lectures, hands-on practicals, and give the opportunity to process your own datasets.

==== Program ====

{{ :2dx-workshop-2016-program-7.pdf |}}


==== Agenda ====

**Workshop will cover a wide variety of topics listed here.**

=== Basic principles of 2D electron crystallography ===

  * Introduction to 2D electron crystallography
  * Cryo-electron microscopy sample preparation for 2D crystals of membrane proteins
  * Cryo-EM data collection of 2D crystals
  * Introduction to 2DX
  * Drift correction using ZORRO  

=== Basic image processing ===

  * Determination of the defocus, crystal tilt geometry, crystal lattice
  * Crystal Unbending - including movie-mode drift correction of individual unit cells in dose-fractionated image series
  * 2D merging and 3D merging with reconstruction via weighted back projection 
  * Automation of the processing pipeline

===  Advanced topics in image processing ===

  * Approaches for a partial reconstruction of amplitudes and phases inside of the missing cone
  * Processing of 2D crystal unit cells with RELION and FREALIGN, under exploitation of neighborhood correlation of certain image parameters
  * Advanced usage of the 2DX backend library
  * Preparation of final results with quantitative description of statistical values (e.g., resolution) for export to databases (EMDB).


==== Speakers ====

**We are happy to announce the following speakers**

=== External ===

Jan-Pieter Abrahams, Paul Scherrer Institute/University of Basel, Switzerland
Cristina Paulino, Max Planck Institute of Biophysics, Germany
Julia Kowal, ETH Zurich, Switzerland
Eric van Genderen, Paul Scherrer Institute, Switzerland

=== Internal ===

Henning Stahlberg, University of Basel, Switzerland
Philippe Ringler, University of Basel, Switzerland
Mohamed Chami, University of Basel, Switzerland
Robert McLeod, University of Basel, Switzerland
Nikhil Biyani, University of Basel, Switzerland
Ricardo Righetto, University of Basel, Switzerland

==== Organizers ====

=== Administration ===
Karen Bergmann, Karen.Bergmann@UniBAS.ch
Heidi Bronnimann, Heidi.Broennimann@UniBAS.ch

=== Organization ===
Nikhil Biyani, Nikhil.Biyani@UniBAS.ch
Ricardo Righetto, Ricardo.Righetto@UniBAS.ch
Robert McLeod, Robert.McLeod@UniBAS.ch
Henning Stahlberg, Henning.Stahlberg@UniBAS.ch


==== Location ====

**C-CINA, Mattenstrasse 26, Basel, Switzerland**
The workshop will be held in Basel, Switzerland. Basel is situated in the northwestern part of Switzerland on the river Rhine. Please check out wikipedia for more details. 

=== Registration, lectures and practicals ===

All lectures and practicals will take place at C-CINA. The C-CINA laboratory is an outstation of the Biozentrum , which is a part of the University of Basel.  Geographically, the lab is located in the Department of Biosystems Science and Engineering (D-BSSE), which is a branch of the Swiss Federal Institute of Technology (ETHZ). Close Tram stops are Tram 2 and 6, stop "Gewerbeschule" and Bus 30, stop "Mattenstrasse".

==== Computing Requirements ====

We will arrange a MacBook for all the participants which can be used to process data. But unfortunately this MacBook does not have enough hard disk space to process the complete dataset. So we strongly recommend you to bring your own external hard drives (1TB+, USB 3.0). You can also bring in your own MacBook.

=== Software requirements ===
Apart from 2dx, we will use the following software during the workshop and can be downloaded from the links mentioned below:
  * EMAN2: http://blake.bcm.edu/emanwiki/EMAN2
  * CCP4: http://www.ccp4.ac.uk/download/index.php
  * Chimera: https://www.cgl.ucsf.edu/chimera/download.html
  * FREALIGN: http://grigoriefflab.janelia.org/frealign

=== System requirements ===
Minimum requirements for the laptop you bring:
  * Dual Core
  * 4 GB RAM
  * 600 GB+ disk space
  * OSX 10.10 (Yosemite) or OSX 10.11 (El Capitan)

==== Flyer ====

{{ :2dxworkshop2016-flyer.pdf |}}


==== Handouts ====

  * {{ :2dx_gui_userguide-2.pdf |}}
  * {{ :01-2dx-2016-intro-stahlberg.pdf |}}
  * {{ :02-2dx-2016-microscope_hardware_genderen.pdf |}}
  * {{ :03-2dx-2016-fourier-stahlberg.pdf |}}
  * {{ :04-2dx-2016-mrc-software.pdf |}}
  * {{ :05-2dx-2016-ctf-correction.pdf |}}
  * {{ :06-2dx-2016-tilt-geometry.pdf |}}
  * {{ :09-2dx-2016-lattice-determination.pdf |}}
  * {{ :10-2dx-2016-symmetries.pdf |}}
  * {{ :11-2dx-2016-unbending.pdf |}}
  * {{ :12-2dx-2016-unbending-moviemode.pdf |}}
  * {{ :14-2dx-2016-merging-2d.pdf |}}
  * {{ :16-2dx-2016-missingcone_biyani.pdf |}}