For the Staining component the macro applies to the RGB image a “Color Deconvolution” [1] using the vector TBD, on the component image TBD, applies a Gaussian Blur (sigma = TBD) and thresholds it using TBD algorithm [ref autothreshold]. For the Tissue component, the macro converts the RGB image to the HSB color space, applies a Gaussian Blur (sigma = TBD) and thresholds the TBD component using the TBD algorithm [2].

1- Ruifrok, A.C. & Johnston, D.A. (2001), "Quantification of histochemical staining by color deconvolution", Anal. Quant. Cytol. Histol. 23: 291-299, PMID 11531144
2- Autothreshold in FIJI

NB: If a ROIset is associated to the image the measurements are restricted to them.

How to Install

Please, use the PTBIOP update site to do the installation and keep up to date.

or have fun with the sources !

How to use

To do so you'll have to :

set a folder
open image and its associated ROIset (if existing).
Define (Save or Load) some Settings
Test the current setting on the current image (showing intermediate images to allow you to affine them)
Process the current image ,or folder.