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
