= BIOP Immunohistochemistry (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|

= BIOP Immunohistochemistry (IHC) Ratio Quantification = {F5943500, layout=right, float, size=full} == What is it ? == The action bar `BIOP IHC Ratio` 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|

= BIOP Immunohistochemistry (IHC) Ratio Quanti=tification = {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|