Biomat

Biomat (ImageJ)
Author Jiří Janáček
Maintainer Jiří Janáček
Source on GitHub
Initial release 03/26/2019
Latest version 03/26/2019


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.

Lipschitz 3D Filter - top hat - subtracts slowly varying background calculated as lower Lipschitz envelope from the image.

Preprocessing example: Image of capillaries in brain

  • Plugins  › Biomat  › Stack Linear Contrast with parameters (multiplyers) "first"= 1.0 and "last"= 3.0
  • Process  › Filters  › Gaussian blur 3D with "sigma"= 1 pixel
  • Plugins  › Biomat  › Lipschitz 3D Filter with parameter "slope"= 2 / pixel

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.

  • Plugins  › Biomat  › Tensor Line 3D Filter with "sigma" set to 3 pixels
  • Image  › Adjust  › Brightness/Contrast
  • 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.

Example: Image of capillaries in embryonic heart.

  • Plugins  › Biomat  › Vector Line 3D Filter with parameters "sigma"= 4 pixels, "scale number"= 2