Walkthrough on localized reconstruction - Revision history

Raffaele Coray: /* Full resolution reconstruction */

2025-12-03T15:24:46Z

Full resolution reconstruction

2024-12-03T12:48:36Z

Download tilt series file

2024-12-02T12:53:34Z

2022-08-08T14:44:59Z

2022-08-08T14:43:54Z

2018-08-27T09:57:30Z

2017-11-13T16:02:47Z

Refining the full resolution reconstruction

2017-11-13T16:02:33Z

Refining the full resolution reconstruction

2017-11-13T16:01:47Z

Computation

2017-11-13T16:01:27Z

Interactive GUI

@@ Line 288: / Line 288: @@
 [[ File:LocalizedWBPlocalReconstruction1Full.png |thumb|center|500px|  Single gold bead, full resolution ]]
-Note that we don't really need to  use the object <tt>fgb</tt> as support. Its only role is to work out the geometry, computing the position of the 3d stack center with reference to the subtomogram that we want to reconstruct locally. We can work out the maths and compute the vector:  <tt>[1035.431 551.378 318.140] </tt>. We could use this vector directly in <tt>dpktilt.math.backproject</tt>
+Note that we don't really need to  use the object <tt>fgb</tt> as support. Its only role is to work out the geometry, computing the position of the 3d stack center with reference to the subtomogram that we want to reconstruct locally. We can work out the maths and compute the vector:  <tt>[1035.431 551.378 318.140] </tt> for a specific gold bead. We could use this vector directly in <tt>dpktilt.math.backproject</tt>
 and get the same result.

@@ Line 18: / Line 18: @@
 The aligned tilt series  can be download with the command:
-  <tt>wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/t6ss/vc17_align.mrc </tt>
+ <!--<tt>wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/t6ss/vc17_align.mrc </tt>-->
 in a linux shell, or through:
-  <tt>curl -O  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/t6ss/vc17_align.mrc</tt>
+  <!--<tt>curl -O  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/t6ss/vc17_align.mrc</tt>-->
 under MacOS.

← Older revision		Revision as of 12:53, 2 December 2024
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		+	[[Category:Walkthroughs]]

	In this walkthrough, we use ''localized reconstruction'' to reconstruct a set of subtomograms at full pixel resolution without the requirement of creating a full reconstruction first.		In this walkthrough, we use ''localized reconstruction'' to reconstruct a set of subtomograms at full pixel resolution without the requirement of creating a full reconstruction first.

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 The position of gold beads in 3d is the addition of the computed shifts (columns 4 to 6 in the table) on the coarse positions of the gold beads:
-  <tt>gf3d = t(:,4:6)+gb*2^3;</tt>
+  <tt>gf3d = t(:,4:6)/(2^3)+gb;</tt>
   <nowiki>r2coarse = outputBP.point3dInAlignedMicrograph(gf3d,'*');

@@ Line 65: / Line 65: @@
 We bin the original tilt series:
-  <tt>sbin = dpktilt.bin(ts,3;)</tt>
+  <tt>sbin = dpktilt.bin(ts,3);</tt>
 This command applies a binning of level two to the micorgraphs in the matrix <tt>ts</tt> separately. Note that the dimensions of the new matrix are floor( [sx,sy]/2<sup>2<2>).

@@ Line 65: / Line 65: @@
 We bin the original tilt series:
-  <tt>sbin = dpktilt.bin(ts,3)</tt>
+  <tt>sbin = dpktilt.bin(ts,3;)</tt>
 This command applies a binning of level two to the micorgraphs in the matrix <tt>ts</tt> separately. Note that the dimensions of the new matrix are floor( [sx,sy]/2<sup>2<2>).
@@ Line 73: / Line 73: @@
 In this walkthrough, we use Weighted Backprojection as reconstruction algorithm. We apply here the simplest possible  filter onto the original projections: a ramp filter.
-   <tt>sf = dpktomo.rec.applyRampFilter(sbin)</tt>
+   <tt>sf = dpktomo.rec.applyRampFilter(sbin);</tt>
 === Reconstruction ===
@@ Line 86: / Line 86: @@
 The reconstruction can be normally accessed through the field <tt>rec</tt> in the output.
-  <tt>dtmshow(outputBP.rec)</tt>
+  <tt>dtmshow(outputBP.rec);</tt>
 [[ File:LocalizedProjectionDtmshowRec.png  |thumb|center|800px|  <tt>tmshow</tt> on the reconstruction, ''z'' and ''x' views ]]

@@ Line 322: / Line 322: @@
   <nowiki> dvunfold goldAligner
-  goldAligner</nowiki>
+ goldAligner</nowiki>
 Then we can check the result.

@@ Line 344: / Line 344: @@
   <tt>gf3d = t(:,4:6)+gb*2^3;</tt>
-  <nowiki>r2coarse= obp.point3dInAlignedMicrograph(gf3d,'*');
+  <nowiki>r2coarse = outputBP.point3dInAlignedMicrograph(gf3d,'*');
-sc     = dpktilt.aux.markgold.MarkerSet();
+sc = dpktilt.aux.markgold.MarkerSet();
 sc.setFrameCellArray(r2coarse);
 ogc = dmarkers(sbin,'lm',sc); </nowiki>

@@ Line 189: / Line 189: @@
 To find the 2d coordinates of all the goldbeads at once in the micrograph corresponding to a tilt angle of -60, we would write
-<nowiki>tilt = 1;
+ <nowiki>tilt = 1;
 r2d = dpktilt.point3dInMicrograph(gb,tiltAngles(tilt),'sizeStack',size(sf),'sc',[200.5,150.5,100.5]);</nowiki>

@@ Line 231: / Line 231: @@
 The basic tool for visualizing sets of 2d markers defined on a tilt series is <tt>dmarkers</tt>. This allows to navigate at once through all the annotations on all the images. We first compute the positions  in 2d of all the 3d positions in <tt>gb</tt>:
-  <nowiki>r2dAll = obp.point3dInAlignedMicrograph(gb,'*');</nowiki>
+  <nowiki>r2dAll = outputBP.point3dInAlignedMicrograph(gb,'*');</nowiki>
 and then create a shape set object with this information. This step is necessary to provide <tt>dmarkers</tt> with the right format.