Programmatic reconstruction of tomograms - Revision history

Daniel Castaño at 09:10, 3 July 2018

2018-07-03T09:10:53Z

Daniel Castaño at 09:55, 2 July 2018

2018-07-02T09:55:45Z

Daniel Castaño at 08:17, 28 June 2018

2018-06-28T08:17:24Z

Daniel Castaño at 08:09, 28 June 2018

2018-06-28T08:09:16Z

Daniel Castaño: 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..."

2018-06-27T16:34:34Z

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..."

New page

''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 <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.
* Filtering of the aligned stack.
* Backprojection of the filtered aligned stack .

== Creation of aligned stacks ==

=== Creation of an aligner object ===

=== Applying the an aligner object ===

=== Use of the alignment object ===

== Weighting of aligned aligned stacks ==

The aligned stack cannot be directly backprojected. There are two ways to reweight its Fourier components so that <tt>aligned.mrc</tt> can be used to create
* Ramp filtering
* Sirt-like filer

=== For weighted back projection ===

=== For sirt-like filtering ===

@@ Line 32: / Line 32: @@
   <tt>f.setCenter([nx,ny]);</tt>
-where ''nx'' and ''ny'' are the ''sidelength'' of the micrographs. Then you create a fit, i.e., search for alignment parameters that best fit the markers.
+where ''nx'' and ''ny'' are the ''sidelength'' of the micrographs. Then you create a fitting, i.e., you instruct the fitter object <tt>f</tt> to search for alignment parameters that best fit the markers.
   <tt>f.linearScan();</tt>
@@ Line 52: / Line 52: @@
 The aligned stack cannot be directly backprojected. There are two ways to reweight its Fourier components so that <tt>aligned.mrc</tt> can be used to create
 * Ramp filtering
-* Sirt-like filer
+* Sirt-like filter
 === For weighted back projection ===
-=== For sirt-like filtering ===
+ <tt>stackWBP =dpktomo.rec.applyRampFilter(alignedStack); </tt>

@@ Line 8: / Line 8: @@
 * Filtering of the aligned stack.
 * Backprojection of the filtered aligned stack .
 == Creation of aligned stacks ==
@@ Line 21: / Line 20: @@
 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 ====

@@ Line 12: / Line 12: @@
 == 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'
+An aligned stack is created by rotating, then shifting each of the slices of a stack.
 === The  aligner object ===
-==== From a set of markers ====
+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.
 ==== 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 ===

@@ Line 3: / Line 3: @@
 == 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.
+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.
 * Filtering of the aligned stack.
 * Backprojection of the filtered aligned stack .
 == Creation of aligned stacks ==
-=== Creation of an aligner object ===
+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'
 === Applying the an aligner object ===
-=== Use of the alignment object ===
+The method <tt>applyOnStack</tt> can be used on a stack (expressed as a variable) to produce the aligned stack.
 == Weighting of aligned aligned stacks ==