= BIOP IHC RatioQuanti=
{F5943500, layout=right, float, size=full}
== What is it ? ==
The action bar `BIOP IHC RatioQuanti` is a simple but versatile tool relying on :
- [[ http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:action_bar:start | `Action Bar` ]] plugin
- `BIOP library`
- `Color Deconvolution` plugin
== What does it ? ==
It allows you to measure the Areas of a **Staining** and of the **Tissue**.
== Why measuring Tissue? ==
(IMPORTANT) You'll find on this page the BIOP recommendation regarding [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/teaching/dab-intensity/ | DAB measurements ]].
== Method ==
**//TBD//** stands for "To Be Defined" in the parameters.
(NOTE)
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), [[ https://www.ncbi.nlm.nih.gov/pubmed/11531144 | "Quantification of histochemical staining by color deconvolution"]], Anal. Quant. Cytol. Histol. 23: 291-299, PMID 11531144
2- [[ http://imagej.net/Auto_Threshold | Autothreshold ]] in FIJI
**NB:** If a ROIset is associated to the image the measurements are restricted to them.
== How to Install ==
Please, use the [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/imagej_tools/update-site/ | PTBIOP update site ]] to do the installation and keep up to date.
or have fun with the [[ https://c4science.ch/source/ijab-biop-ihc-ratioquanti/ | 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.
== Settings==
=== Specify ===
{F5906433, size = full}
=== Save/Load ===
{F5906440, size = full}
== Test ===
{F5906449, size = full}
== Process ==
{F5906463, size = full}
In cas Image has a ROIset
{F5906468, size = full}
== HELP ==
For futher help please [[ https://biop.epfl.ch/INFO_Facility.html#staff | contact ]] us or open an [[ https://github.com/PTBIOP/ijab-biop-ihc-ratioquanti/issues |issue]] on github.
| Main Developer | Romain Guiet |
| Maintainers | Romain Guiet, Oliver Burri|