View source for Pipelines for Workshop Heidelberg 2018

These materials describe the procedural steps required for high resolution tomography. 


= Pipeline = 

== Input data ==
We will start with two tilt series.  A drift correction has already been applied on each tilt using motioncorr2, so that each micrograph in a tilt series is an averaged movie.  The pixel size is 2.7A (the tilt series have been binned by fourier cropping to ease the computation ), and the structures of interest form spherical lattices.

== Procedural steps ==

=== Preprocessing steps ===
As we will initially work with already drift-corrected tilt series, 
* Defocus estimation with <tt>ctffind4</tt>
* Alignment of tilt series with ''Dynamo''
* Exposure filter on the aligned tilt series. 
* Stripe-based CTF correction  (with <tt>ctfphaseflip</tt> from Imod)
* Creation of tomograms with ''Dynamo''

These preprocessing  operations that go from the tilt series to the tomograms can be used for any sample.

=== Tomogram management ===

This part is specific to the particular geometry of the proteins of interest. 
* Cataloguing the tomograms (archiving)
* Annotation of vesicle positions.
* Extraction of  putative particles based on the vesicle positions.
* Ellimination of repeated particles.

=== Subtomogram averaging ===

* Extraction of true particles.
* Splitting in odd and even data sets.
* Independent alignment and resolution determination.

= Material organization =

The data corresponding to each tilt series is under the folders <tt>work/1</tt>  and  <tt>work/2</tt>.  Intermediate results corresponding to each tilt series will be stored in the corresponding folders. 

The initial structure of the folder contains two items 

 <pre>ls work/1
rawStack.mrc
nominalTilts.tlt
</pre>

 The additional processing steps will gradually generate more elements pert tilt.

== Copying data  to your account ==

You will need to copy the provided data into you account:

 <tt>cp -r /g/embl/workshop/teach11/data/work  . </tt> 

== Matlab environment == 

Matlab provides a convenient syntax for manipulation of sets of paths. 

== Preprocessing ==
Each of the preprocessing steps can be computed separately for each tilt series. We have thus provided a set of functions, each one a wrapper that accepts as input one index that identifies a tilt series and creates an output with the right naming convention.
They are intended to be callable on a loop like:

 <pre> for i=1:2
emboFunction('work',i);
end </pre>

If new tilt series are added to increase resolution, you just need to apply the function on additional indices.

===  defocus estimation ===

The function <tt>emboDefocusEstimation</tt> will run <tt>ctffind4</tt> on the input data, creating the following items

* Input:
* Output:

===  tilt series alignment ===
* Input:
* Output:
 
===  dose filtering ===
* Input:
* Output:

===  CTF correction of tilt series ===
* Input:
* Output:

===  Reconstruction of tomogram ===
* Input:
* Output:

== Management of tomogram data ==


== Subtomogram averaging ==