Differences

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--- plugin:utilities:layers_analysis:start [2019/08/29 07:40] – [Saving the results and cleaning temporary files] tboudier
+++ plugin:utilities:layers_analysis:start [2019/09/12 04:24] (current) – [Layers analysis] tboudier
@@ Line 7: / Line 7: @@
 The **EVF** (Eroded Volume Fraction) can be regarded as a //normalized// **EDT** (Euclidean Distance Map), it was first described in [[https://onlinelibrary.wiley.com/doi/full/10.1002/jcb.21823|this article]]. The **[[https://en.wikipedia.org/wiki/Distance_transform|EDT]]** will compute for each pixel inside the structure of interest the **distance to the border** of the structure and output a map where the pixel value is actually the distance.
-Here we assume you already have a binarised structure image with value 0 for the background. First we need to **input** the binary image of the structure, compute the **EVF** and **save** it locally. The input data can either be a file on disk or an image in a OMERO database as explained in the [[plugin:utilities:tapas_tutorial_:input_output_i:start|tutorial on Input/Output]].
+Here we assume we already have a binarised structure image with value 0 for the background. First we need to **input** the binary image of the structure, compute the **EVF** and **save** it locally. The input data can either be a file on disk or an image in a OMERO database as explained in the [[plugin:utilities:tapas_tutorial_:input_output_i:start|tutorial on Input/Output]].
 <code>
 // We use here the raw data as the reference image and
-// we assume the binary image has the same name as the reference image with -structure
+// we assume the binary image has the same name
+// as the reference image with -structure
 process:input
 name:?name?-structure
@@ Line 27: / Line 28: @@
 file:?name?-evf.tif
 </code>
 {{:plugin:stacks:3d_ij_suite:evf-bin.png?direct&256|Binary image}}
@@ Line 33: / Line 33: @@
 ==== Layers analysis ====
-The values in the EVF are normalized between 0 and 1 and then can be used to compute layer distribution inside many structures regardless of their size. Furthermore, in case of a random distribution the distribution within EVF layers should be flat since, in EVF, all layers have equal volume. Note that using EDT to compute distribution within layers may lead to biased results, since volumes based on distance to border will not have equal volumes. Compare the EVF on the left and the EDT on the right.
+The values in the EVF are normalized between 0 and 1 and, then can be used to compute layer distribution inside many structures regardless of their size. Furthermore, in case of a random distribution the distribution within EVF layers should be flat since, in EVF, all layers have equal volume. Note that using EDT to compute distribution within layers may lead to biased results, since volumes based on distance to border will not have equal volumes. Compare the EVF on the left and the EDT on the right.
 {{:plugin:stacks:3d_ij_suite:evf-evf.png?direct&256|EVF image}}
 {{:plugin:stacks:3d_ij_suite:evf-edt.png?direct&256|EDT image}}
-We will use the **evfLayers** module to compute distribution of spots within a fixed number of layers (of equal volume) within the EVF image. We need to define the number of layers and the path to the corresponding EVF image. The input for the evfLayers analysis should be a binary or labelled image of the spots, the module will compute in each layer the volume occupied by the spots.
+We will use the **evfLayers** module to compute distribution of spots within a fixed number of layers (of equal volume) within the EVF image. We need to define the number of layers and the path to the corresponding EVF image. The input for the **evfLayers** analysis should be a binary or labelled image of the spots, the module will compute in each layer the volume occupied by the spots.
 <code>
@@ Line 48: / Line 48: @@
 // layer analysis
-// path ot the previously saved evf image
+// path to the previously saved evf image
 // and where to save the results
 // and number of layers (100 by default)
@@ Line 59: / Line 59: @@
 </code>
-The output of the evfLayers module will be first the plot and values for the raw data, respectively as PNG and csv file. In this example with 100 layers, a perfect random distribution should be flat with value 0.01. We can then see in this example a trend toward low evf values, indicating that the spots are mostly localized near the border of the structure.
+The output of the evfLayers module will be first the plot and values for the input data, respectively as PNG and csv file. In this example with 100 layers, a perfect random distribution should be flat with value 0.01. We can then see in this example a trend toward low evf values, indicating that the spots are mostly localized near the border of the structure.
-{{:plugin:stacks:3d_ij_suite:evf-plot.png?direct&400|EVF layer plot}}
+{{:plugin:stacks:3d_ij_suite:evf-plot.png?direct&600|EVF layer plot}}
-The module will also output with the suffix -all the plot and volumes of the different layers, due to numerical approximation the volumes of all layers are not exactly equal, this output can be hence used for further normalisation.
+The module will also output with the suffix //-all// the plot for volumes of the different layers, due to numerical approximation, the volumes of the layers are not exactly equal, this output can be hence used for further normalisation.
-{{:plugin:stacks:3d_ij_suite:evf-plot-all.png?direct&400|EVF layer plot all}}
+{{:plugin:stacks:3d_ij_suite:evf-plot-all.png?direct&600|EVF layer plot all}}
 ==== Saving the results and cleaning temporary files ====