Merge pull request #344 from jiri-janacek/patch-1

Patch 1

_pages/plugins/biomat.md

@@ -18,34 +18,39 @@ source-url: https://github.com/jiri-janacek/biomat
 
 **Lipschitz 3D** Filter - top hat - subtracts slowly varying background calculated as lower Lipschitz envelope from the image.
 
-Preprocessing example: [Image of capillaries in brain](/media/plugins/capillaries-brain.zip)
+Preprocessing example: [Stack of confocal microscopy images of capillaries in rat brain](/media/plugins/capillaries-brain.zip)
 
 -   {% include bc path='Plugins | Biomat | Stack Linear Contrast'%} with parameters (multiplyers) "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 parameter "slope"= 2 / pixel
+-   {% include bc path='Plugins | Biomat | Lipschitz 3D Filter'%} with parameter "slope"= 2
 
 ## Plugins for detection of fibres in 3D image
 
 **Tensor Line 3D Filter** - enhances white fibers of uniform width sparsely distributed on dark background.
 
-Example: [Image of capillaries in adipose tissue](/media/plugins/capillaries-adipose.zip).
+Example: [Stack of confocal microscopy images of capillaries in adipose tissue](/media/plugins/capillaries-adipose.zip).
 
 -   {% include bc path='Plugins | Biomat | Tensor Line 3D Filter'%} with "sigma" set to 3 pixels
 -   {% include bc path='Image | Adjust | Brightness/Contrast'%}
 -   {% include bc path='Process | Filters | Gaussian blur 3D'%} with "sigma"= 1 pixel
 
-**Vector Line 3D Filter** - enhances white fibers of varying thickness. Crossection of the fibers need not be circular. Parameter "sigma" in pixels corresponds to the largest diameter.
+**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.
 
-Example: [Image of capillaries in embryonic heart](/media/plugins/capillaries-heart.zip).
+Example: [Stack of MicroCT images of capillaries in embryonic heart](/media/plugins/capillaries-heart.zip).
 
 -   {% include bc path='Plugins | Biomat | Vector Line 3D Filter'%} with parameters "sigma"= 4 pixels, "scale number"= 2
 
-## Plugins for evaluation of 2D images using heat equation
-
-**2D Tensor Color Coding** - standard color coding of 2D tensor image. Symmetric tensor is coded as channels of 32 bit image stacks.
+## Plugins for evaluation of directionality of 2D binary images using heat equation
 
 **2D Heat Kernel Tensor** - second order moments of heat kernel calculated from 8 bit binary image.
 
+**2D Tensor Color Coding** - standard color coding of 2D tensor image. Symmetric tensor is coded as channels of 32 bit image stacks.
+
 **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.
 
+Example: [Projection of binary images of capillaries in brain](/media/plugins/MAX_2_4cortexa1.tif).
+
+-   {% include bc path='Plugins | Biomat | 2D Heat Kernel Tensor'%}
+-   {% include bc path='Plugins | Biomat | 2D Tensor Statistics'%}
+-   {% include bc path='Process | Biomat | 2D Tensor Color Coding'%}