Difference between revisions of "Programmatic reconstruction of tomograms"

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(Created page with "''Dynamo'' includes several tools for creation of tomograms from initial tilt series. This articles presents an overview of the tools that can be used from the command line or...")
 
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== Overview ==
 
== Overview ==
  
We assume that a raw tilt series  <tt>raw.mrc</tt> is available, and also a set of markers that indexes the gold fiducials.  Given this input, the creation of a tomogram will involve these steps.  
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We assume that a raw tilt series  <tt>'raw.mrc'</tt> is available, and also a set of markers that indexes the gold fiducials.  Given this input, the creation of a tomogram will involve these steps.  
  
 
* Creation of an aligned stack.
 
* Creation of an aligned stack.
 
* Filtering of the aligned stack.
 
* Filtering of the aligned stack.
 
* Backprojection of the filtered aligned stack .
 
* Backprojection of the filtered aligned stack .
 +
  
 
== Creation of aligned stacks ==
 
== Creation of aligned stacks ==
  
=== Creation of an aligner object ===
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An aligned stack is created by rotating, then shifting each of the slices of a stack.  This procedure can be driven through an object of the class 'stackAligner'
 +
 
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=== The  aligner object ===
 +
 
 +
==== From a set of markers ====
 +
 
 +
==== Programmatically ====
 +
 
 +
Stack aligners don't need to be extracted from a <tt>fitter</tt> object. If you computed your alignment parameters in any other way, you can still
  
 
=== Applying the an aligner object ===
 
=== Applying the an aligner object ===
  
=== Use of the alignment object ===
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The method <tt>applyOnStack</tt> can be used on a stack (expressed as a variable) to produce the aligned stack.
 +
 
 +
<tt>alignedStack = stackAligner.applyOnStack('rawStack.mrc')</tt>
  
 
== Weighting of aligned aligned stacks ==
 
== Weighting of aligned aligned stacks ==

Revision as of 08:09, 28 June 2018

Dynamo includes several tools for creation of tomograms from initial tilt series. This articles presents an overview of the tools that can be used from the command line or inside scripts created by the users.

Overview

We assume that a raw tilt series 'raw.mrc' is available, and also a set of markers that indexes the gold fiducials. Given this input, the creation of a tomogram will involve these steps.

  • Creation of an aligned stack.
  • Filtering of the aligned stack.
  • Backprojection of the filtered aligned stack .


Creation of aligned stacks

An aligned stack is created by rotating, then shifting each of the slices of a stack. This procedure can be driven through an object of the class 'stackAligner'

The aligner object

From a set of markers

Programmatically

Stack aligners don't need to be extracted from a fitter object. If you computed your alignment parameters in any other way, you can still

Applying the an aligner object

The method applyOnStack can be used on a stack (expressed as a variable) to produce the aligned stack.

alignedStack = stackAligner.applyOnStack('rawStack.mrc')

Weighting of aligned aligned stacks

The aligned stack cannot be directly backprojected. There are two ways to reweight its Fourier components so that aligned.mrc can be used to create

  • Ramp filtering
  • Sirt-like filer

For weighted back projection

For sirt-like filtering