Framework for estimation of membrane thickness - Revision history

Daniel Castaño: /* Applying the filters onto a particle */

2017-05-09T10:09:51Z

Applying the filters onto a particle

2017-05-09T10:07:48Z

Creating distance filters

2017-05-09T10:04:36Z

Checking the read particles

2017-05-09T10:00:45Z

Reading the particles

2017-05-09T10:00:06Z

2017-05-09T09:56:18Z

2017-05-09T09:56:05Z

2017-05-04T10:47:38Z

Creating distance filters

2017-05-04T10:46:44Z

2017-05-04T10:41:52Z

Loop on particles and distance histogram

@@ Line 97: / Line 97: @@
 </nowiki>
-In particular, <tt>ccmax</tt> is telling you the response of the particle to each filter. In this case, the largest response is to the third filter in <tt>t</tt>, corresponding to an space of 5 pixels.
+In particular, <tt>ccmax</tt> is telling you the response of the particle to each filter. In this case, the largest response is to the third filter in <tt>t</tt>, corresponding to an space of 5 pixels. Note that in this particle the maximum of the cc is significantly bigger for one filter than for the others. Ideally, most of your particles should behave this way.
 == Loop on particles and distance histogram==

@@ Line 70: / Line 70: @@
   <tt> t = dpkfw.mdm.templateSeries('size',[16,16,16],'thickness',1,'distance',[3:7]); </tt>
-Here, <tt>t</tt> is a [[cell array]], containing 5 volumes of 16x16x16 pixels each. Each volume contains a "model" of a membrane. You can visualize them with:
+Here, <tt>t</tt> is a [[matlab cell array | cell array]], containing 5 volumes of 16x16x16 pixels each. Each volume contains a "model" of a membrane. The different models are coded with the flag  <tt>distance</tt>. In this case, the  model number one contains a membrane which a distance between layers  of 3 pixels. In the last model, the distance is 7.
   <tt>figure;dslices(t,'projy','*','dim',[1,5]);</tt>
-[[File:MembraneDistanceFilters.png|thumb|center|300px| Y projections of the five filters]]
+[[File:MembraneDistanceFilters.png|thumb|center|400px| Y projections of the five filters, with distances from 3 to 7 pixels]]
 == Applying the filters onto a particle ==

@@ Line 60: / Line 60: @@
   <nowiki>
 myAverage = dynamo_sumarray(pac);
-dview(myAverage);
+dview(myAverage);</nowiki>
-[[File:MembraneThicknessAverage.png|thumb|center|300px| Histogram of best responding membrane filters]]
+[[File:MembraneThicknessAverage.png|thumb|center|500px| Y-view of the averaged membrane]]
 == Creating distance filters==

@@ Line 6: / Line 6: @@
   <nowiki>ddb myProject:rt -d # prints in screen the last available refined table
- ddb myProject:data -d%;</nowiki>
+ddb myProject:data -d % prints on screen the data folder linked to this project;</nowiki>
 In any case,
@@ Line 64: / Line 64: @@
 [[File:MembraneThicknessAverage.png|thumb|center|300px| Histogram of best responding membrane filters]]
-−
 == Creating distance filters==

@@ Line 3: / Line 3: @@
 == Reading the particles ==
-The easiest way to bring particles aligned by a project is through the use of the  <tt>dpkdata.Reader</tt> object. If you store the [[table]] and [[data folder]] of your project in <tt>myTable</tt> and <tt>myData</tt>
+The easiest way to bring particles aligned by a project is through the use of the  <tt>dpkdata.Reader</tt> object. First store the [[table]] and [[data folder]] of your project in variables <tt>myTable</tt> and <tt>myData</tt>. This can be easily done by browsing into the folder structure, or just by using <tt>ddb</tt> to extract items from the project. Option <tt>-d<tt> will just display the file or folder location.
   <nowiki >r = dpkdata.Reader();

@@ Line 6: / Line 6: @@
   <nowiki >r = dpkdata.Reader();
-r.setSource('table', myTable,'data',myData);
+r.setSource('table', myTable,'data',myData);</nowiki>
 you can access the particles throught the <tt>getParticle</tt> method:

← Older revision		Revision as of 09:56, 9 May 2017
Line 51:		Line 51:
	</nowiki>		</nowiki>

		+	=== Checking the read particles===
		+
		+	We can only measure the membrane distance on aligned particles. At this point we make certain that everything is ok by quickly adding all the particles in the cell array and checking visually the result.
		+	<nowiki>
		+	myAverage = dynamo_sumarray(pac);
		+	dview(myAverage);
		+	</nowiki>
		+
		+	[[File:MembraneThicknessAverage.png\|thumb\|center\|300px\| Histogram of best responding membrane filters]]
		+
	== Creating distance filters==		== Creating distance filters==

@@ Line 55: / Line 55: @@
 We first create a set of filters that model the distance between the two layers of the membrane.
-  <tt> t = dpkfw.mdm.templateSeries('size',16,'thickness',1,'distance',[3:7]); </tt>
+  <tt> t = dpkfw.mdm.templateSeries('size',[16,16,16],'thickness',1,'distance',[3:7]); </tt>
 Here, <tt>t</tt> is a [[cell array]], containing 5 volumes of 16x16x16 pixels each. Each volume contains a "model" of a membrane. You can visualize them with:

@@ Line 97: / Line 97: @@
 >> ylabel('# Particles');
 </nowiki>
+[[File:MembraneDistanceHistogram.png|thumb|center|300px| Histogram of best responding membrane filters]]
 You'll need to convert each index to the actual number of pixels of the intermembrane space, and of course to physical units.