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Plugins for 3D image preprocessing
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.
Preprocessing example: Stack of confocal microscopy images of capillaries in rat brain
Original data
- Plugins › Biomat › Stack Linear Contrast with “first” = 1.0 and “last” = 3.0
- Process › Filters › Gaussian blur 3D with “sigma” = 1 pixel
- Plugins › Biomat › Lipschitz 3D Filter with “slope” = 2 and “top hat” on
Processed data
Morphological operations with quadratic structuring function
Spherical Extrusion - tool for calculation of volume of objects from 2D projections.
Example: Synthetic contours
Original data
- Plugins › Biomat › Spherical Extrusion
Height of spherical extrusion
Area and mean height of spherical extrusion
Volume = 2 * Area * Mean.
Reconstructed objects
Distance Map 3D - 3D Euclidean distance transform.
Example: Ball with 40 pixels radius
- Plugins › Biomat › Distance Map 3D
Plugins for detection of fibres in 3D image
Tensor Line 3D Filter - enhances white fibers of uniform width sparsely distributed on dark background.
Example: Stack of confocal microscopy images of capillaries in adipose tissue.
Original data
- Plugins › Biomat › Tensor Line 3D Filter with “sigma” = 3 pixels
- Image › Adjust › Brightness/Contrast
- Process › Filters › Gaussian blur 3D with “sigma” = 1 pixel
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.
Original data
Processed data
Example: Stack of MicroCT images of capillaries in rodent embryonic heart.
- Plugins › Biomat › Vector Line 3D Filter with “sigma” = 4 pixels and “scale number” = 2
Plugins for evaluation of directionality in 2D 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.
Binary image
- Plugins › Biomat › 2D Heat Kernel Tensor
- Plugins › Biomat › 2D Tensor Statistics
Statistics
- Process › Biomat › 2D Tensor Color Coding
Color coded tensor image
