Difference between revisions of "Programmatic reconstruction of tomograms"
| Line 12: | Line 12: | ||
== Creation of aligned stacks == | == Creation of aligned stacks == | ||
| − | An aligned stack is created by rotating, then shifting each of the slices of a stack. | + | An aligned stack is created by rotating, then shifting each of the slices of a stack. |
=== The aligner object === | === The aligner object === | ||
| − | ==== | + | This procedure can be driven through an object of the class <tt>'stackAligner'</tt>, designed to contain alignment parameters, and to locate easily functionalities associated with the alignment of stacks. |
| + | |||
| + | ==== Creation from a set of markers ==== | ||
| + | |||
| + | Stack aligner objects can be derived from marker sets. This requires the previous step of fitting the marker set to a 3d projeciton model. | ||
| + | |||
==== Programmatically ==== | ==== 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 | + | 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 create a stack alignment object and fill manually its contents. |
=== Applying the an aligner object === | === Applying the an aligner object === | ||
Revision as of 08:17, 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.
Contents
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.
The aligner object
This procedure can be driven through an object of the class 'stackAligner', designed to contain alignment parameters, and to locate easily functionalities associated with the alignment of stacks.
Creation from a set of markers
Stack aligner objects can be derived from marker sets. This requires the previous step of fitting the marker set to a 3d projeciton model.
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 create a stack alignment object and fill manually its contents.
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
