Merge pull request #346 from jiri-janacek/patch-4

Update biomat.md

_pages/plugins/biomat.md

@@ -3,49 +3,48 @@ mediawiki: Biomat
 name: "Biomat"
 title: Biomat
 categories: [Filtering]
-release-date: "10/17/2024"
+release-date: "10/18/2024"
 initial-release-date: "03/26/2019"
 team-founder: 'Jiří Janáček'
 team-maintainer: 'Jiří Janáček | mailto:jiri.janacek_at_fgu.cas.cz'
 source-url: https://github.com/jiri-janacek/biomat
 ---
 
-
 ## Plugins for 3D image preprocessing
 
-**Stack Linear Contrast** - multiplies images in stack by coefficient obtained by linear interpolation of the "first" and "last" coefficient. A simple tool for compensation of contrast decreasing with depth within thick sample.
+**Stack Linear Contrast** - multiplies images in stack by coefficient obtained by linear interpolation of the "first" and "last" parameter. A simple tool for compensation of contrast decreasing with depth within thick sample.
 
 **Lipschitz 3D** Filter - top hat - subtracts slowly varying background calculated as lower Lipschitz envelope from the image.
 
- {% include img align="right" name="brain" src="https://raw.githubusercontent.com/jiri-janacek/biomat/master/media/capillaries_brain_3Dg.gif" %}
-
- {% include img align="right" name="brain proc" src="https://raw.githubusercontent.com/jiri-janacek/biomat/master/media/capillaries_brain_proc_3Dg.gif" %}
-
 Preprocessing example: [Stack of confocal microscopy images of capillaries in rat brain](/media/plugins/capillaries-brain.zip)
 
+ {% include img align="center" name="brain" src="https://raw.githubusercontent.com/jiri-janacek/biomat/b9b53126134ac7e9fbca9a29de66bc7f2b7c845e/media/capillaries_brain_3Dg.gif" caption="Original data" %}
+
 -   {% include bc path='Plugins | Biomat | Stack Linear Contrast'%} with "first" = 1.0 and "last" = 3.0
 -   {% include bc path='Process | Filters | Gaussian blur 3D'%} with "sigma" = 1 pixel
 -   {% include bc path='Plugins | Biomat | Lipschitz 3D Filter'%} with "slope" = 2 and "top hat" on
 
+ {% include img align="center" name="brain proc" src="https://raw.githubusercontent.com/jiri-janacek/biomat/b9b53126134ac7e9fbca9a29de66bc7f2b7c845e/media/capillaries_brain_proc_3Dg.gif" caption="Processed data" %}
+
 ## Plugins for detection of fibres in 3D image
 
 **Tensor Line 3D Filter** - enhances white fibers of uniform width sparsely distributed on dark background.
 
-{% include img align="right" name="adipose" src="https://raw.githubusercontent.com/jiri-janacek/biomat/master/media/capillaries_adipose_3Dg.gif" %}
-
-{% include img align="right" name="adipose proc" src="https://raw.githubusercontent.com/jiri-janacek/biomat/master/media/capillaries_adipose_proc_3Dg.gif" %}
-
 Example: [Stack of confocal microscopy images of capillaries in adipose tissue](/media/plugins/capillaries-adipose.zip).
 
+{% include img align="center" name="adipose" src="https://raw.githubusercontent.com/jiri-janacek/biomat/b9b53126134ac7e9fbca9a29de66bc7f2b7c845e/media/capillaries_adipose_3Dg.gif" caption="Original data" %}
+
 -   {% include bc path='Plugins | Biomat | Tensor Line 3D Filter'%} with "sigma" = 3 pixels
 -   {% include bc path='Image | Adjust | Brightness/Contrast'%}
 -   {% include bc path='Process | Filters | Gaussian blur 3D'%} with "sigma" = 1 pixel
 
+{% include img align="center" name="adipose proc" src="https://raw.githubusercontent.com/jiri-janacek/biomat/b9b53126134ac7e9fbca9a29de66bc7f2b7c845e/media/capillaries_adipose_proc_3Dg.gif" caption="Processed data" %}
+
 **Vector Line 3D Filter** - enhances white fibers of varying width. Crossection of the fibers need not be circular. Parameter "sigma" in pixels corresponds to the largest diameter.
 
-{% include img align="right" name="heart" src="https://raw.githubusercontent.com/jiri-janacek/biomat/master/media/cardio,3-18_sp.2_rec0.5mov.gif" %}
+{% include img align="center" name="heart" src="https://raw.githubusercontent.com/jiri-janacek/biomat/b9b53126134ac7e9fbca9a29de66bc7f2b7c845e/media/cardio,3-18_sp.2_rec0.5mov.gif" caption="Original data" %}
 
-{% include img align="right" name="heart proc" src="https://raw.githubusercontent.com/jiri-janacek/biomat/master/media/cardio,3-18_sp.2_rec0.5_4_2_3_v3dlin_mov.gif" %}
+{% include img align="center" name="heart proc" src="https://raw.githubusercontent.com/jiri-janacek/biomat/b9b53126134ac7e9fbca9a29de66bc7f2b7c845e/media/cardio,3-18_sp.2_rec0.5_4_2_3_v3dlin_mov.gif" caption="Processed data" %}
 
 Example: [Stack of MicroCT images of capillaries in rodent embryonic heart](/media/plugins/capillaries-heart.zip).
 
@@ -59,15 +58,15 @@ Example: [Stack of MicroCT images of capillaries in rodent embryonic heart](/med
 
 **2D Tensor Statistics** - summary of tensor image (in ROI). "Value" is average trace of the tensor, "shape" is the ratio of its eigenvalues and "angle" of the first eigenvector is measured counterclockwise from the horizontal axis.
 
-{% include img align="right" name="binary" src="https://raw.githubusercontent.com/jiri-janacek/biomat/master/media/MAX_2_4cortexa1.png" %}
-
-{% include img align="right" name="results" src="https://raw.githubusercontent.com/jiri-janacek/biomat/master/media/MAX_2_4cortexa1_res.png" %}
+Example: [Projection of binary images of capillaries in brain](https://raw.githubusercontent.com/jiri-janacek/biomat/b9b53126134ac7e9fbca9a29de66bc7f2b7c845e/media/MAX_2_4cortexa1.tif).
 
-{% include img align="right" name="color" src="https://raw.githubusercontent.com/jiri-janacek/biomat/master/media/MAX_2_4cortexa1_tens_col.png" %}
-
-Example: [Projection of binary images of capillaries in brain](https://raw.githubusercontent.com/jiri-janacek/biomat/master/media/MAX_2_4cortexa1.tif).
+{% include img align="center" name="binary" src="https://raw.githubusercontent.com/jiri-janacek/biomat/b9b53126134ac7e9fbca9a29de66bc7f2b7c845e/media/MAX_2_4cortexa1.png" caption="Binary image" %}
 
 -   {% include bc path='Plugins | Biomat | 2D Heat Kernel Tensor'%}
 -   {% include bc path='Plugins | Biomat | 2D Tensor Statistics'%}
+
+{% include img align="center" name="results" src="https://raw.githubusercontent.com/jiri-janacek/biomat/b9b53126134ac7e9fbca9a29de66bc7f2b7c845e/media/MAX_2_4cortexa1_res.png" caption="Statistics" %}
+
 -   {% include bc path='Process | Biomat | 2D Tensor Color Coding'%}
 
+{% include img align="center" name="color" src="https://raw.githubusercontent.com/jiri-janacek/biomat/b9b53126134ac7e9fbca9a29de66bc7f2b7c845e/media/MAX_2_4cortexa1_tens_col.png" caption="Color coded tensor image" %}