= Documentaion = You can find all the [[ https://github.com/qupath/qupath/wiki/ | documentation ]] on-line. =1. Install = [[https://github.com/qupath/qupath/releases/ | Download the latest release]] corresponding to your operating system ( Windows / OSX / Linux) and [[ https://github.com/qupath/qupath/wiki/Extensions | add some extensions ]], at least the [[ https://github.com/qupath/qupath-bioformats-extension | BioFormats extension ]] (you have 2 files to download and to Drag&Drop on QuPath window) . == QuPath Latest Versions == The BIOP is maintaining the current version with the latest bugfixes at (NOTE)**\\svfas6.epfl.ch\biop\public\0 - BIOP Data\0-Install\QuPath\0.1.3-SNAPSHOT** Just copy paste the folder to your favorite location and run `QuPath.exe` (WARNING) **MAC **Users can get the compiled version at **smb://svfas6.epfl.ch/biop/public/0 - BIOP Data/0-Install/QuPath/0.1.3-SNAPSHOT MAC** =2. Create a project= ==Description== For images of a Project to be accesible from different computers they have to be within the project folder. **BUT** when you create a project you can only select an `empty` folder! ==Recommended procedure to create a Project== |**Step Number**|**Explorer** (or Finder with OSX)|**QuPath**|//notes//| |1| Make a new folder corresponding to the //`project name`//| | | |2||clic {key Create_project}, follow path to this folder {key Select_folder}|// it has to be an empty folder//| |3|`Copy` your images within this folder, by creating a subfolder `images`||// to be readable on several computers, the images have to be in a subfolder of the project folder//| |4||clic {key Add_images}, select images from the folder `images`|//you can add one, or several, image(s) at a time, more details in [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/import_vsi/ | 3. Import VSI]]//| ==Procedure to open a project== Now, everyone (with "reading" right to the destination folder) can access the images from every computer: # Start QuPath # Press {key Open_project} # Double-clic on the thumbnail image =3. Import VSI= First, you need to install the [[ https://github.com/qupath/qupath-bioformats-extension | BioFormats extension ]]. Then you can follow these [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/import_vsi/| instructions ]]. =4.Export annotations within QuPath= Using [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/export_annotations_groovy/| Groovy script]] works for 1 image or 1 project. Using [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/export_annotations_imagej/| ImageJ macro]] works for 1 image =5. Image Processing & Analysis = ==5.1 Color Deconvolution == === using QuPath === [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/define-stain-vectors/ |tutorial ]] === using ImageJ Plugin combined with Threshold == Using the ImageJ plugin through [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/color_decon_threshold/ | ImageJ macro]] == 5.2 Analyse by Annotations names == A Groovy [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/qps-analysis_by_annotationclasses/ | script ]] for QuPath

= Documentaion = You can find all the [[ https://github.com/qupath/qupath/wiki/ | documentation ]] on-line. =1. Install = [[https://github.com/qupath/qupath/releases/ | Download the latest release]] corresponding to your operating system ( Windows / OSX / Linux) and [[ https://github.com/qupath/qupath/wiki/Extensions | add some extensions ]], at least the [[ https://github.com/qupath/qupath-bioformats-extension | BioFormats extension ]] (you have 2 files to download and to Drag&Drop on QuPath window) . == QuPath Latest Versions == === Win 10 === The BIOP is maintaining the current version with the latest bugfixes at (NOTE)**\\svfas6.epfl.ch\biop\public\0 - BIOP Data\0-Install\QuPath\0.1.3-SNAPSHOT** Just "Copy & Paste" the folder to your favorite location and run `QuPath.exe` === Mac OSX === (WARNING) Get the compiled version at **smb://svfas6.epfl.ch/biop/public/0 - BIOP Data/0-Install/QuPath/0.1.3-SNAPSHOT MAC** =2. Create a project= ==Description== For images of a Project to be accesible from different computers they have to be within the project folder. **BUT** when you create a project you can only select an `empty` folder! ==Recommended procedure to create a Project== |**Step Number**|**Explorer** (or Finder with OSX)|**QuPath**|//notes//| |1| Make a new folder corresponding to the //`project name`//| | | |2||clic {key Create_project}, follow path to this folder {key Select_folder}|// it has to be an empty folder//| |3|`Copy` your images within this folder, by creating a subfolder `images`||// to be readable on several computers, the images have to be in a subfolder of the project folder//| |4||clic {key Add_images}, select images from the folder `images`|//you can add one, or several, image(s) at a time, more details in [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/import_vsi/ | 3. Import VSI]]//| ==Procedure to open a project== Now, everyone (with "reading" right to the destination folder) can access the images from every computer: # Start QuPath # Press {key Open_project} # Double-clic on the thumbnail image =3. Import VSI= First, you need to install the [[ https://github.com/qupath/qupath-bioformats-extension | BioFormats extension ]]. Then you can follow these [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/import_vsi/| instructions ]]. =4.Export annotations within QuPath= Using [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/export_annotations_groovy/| Groovy script]] works for 1 image or 1 project. Using [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/export_annotations_imagej/| ImageJ macro]] works for 1 image =5. Image Processing & Analysis = ==5.1 Color Deconvolution == === using QuPath === [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/define-stain-vectors/ |tutorial ]] === using ImageJ Plugin combined with Threshold == Using the ImageJ plugin through [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/color_decon_threshold/ | ImageJ macro]] == 5.2 Analyse by Annotations names == A Groovy [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/qps-analysis_by_annotationclasses/ | script ]] for QuPath

= Documentaion = You can find all the [[ https://github.com/qupath/qupath/wiki/ | documentation ]] on-line. =1. Install = [[https://github.com/qupath/qupath/releases/ | Download the latest release]] corresponding to your operating system ( Windows / OSX / Linux) and [[ https://github.com/qupath/qupath/wiki/Extensions | add some extensions ]], at least the [[ https://github.com/qupath/qupath-bioformats-extension | BioFormats extension ]] (you have 2 files to download and to Drag&Drop on QuPath window) . == QuPath Latest Versions == === Win 10 === The BIOP is maintaining the current version with the latest bugfixes at (NOTE)**\\svfas6.epfl.ch\biop\public\0 - BIOP Data\0-Install\QuPath\0.1.3-SNAPSHOT** Just copy p"Copy & Paste" the folder to your favorite location and run `QuPath.exe` (WARNING) **MAC **Users can get=== Mac OSX === (WARNING) Get the compiled version at **smb://svfas6.epfl.ch/biop/public/0 - BIOP Data/0-Install/QuPath/0.1.3-SNAPSHOT MAC** =2. Create a project= ==Description== For images of a Project to be accesible from different computers they have to be within the project folder. **BUT** when you create a project you can only select an `empty` folder! ==Recommended procedure to create a Project== |**Step Number**|**Explorer** (or Finder with OSX)|**QuPath**|//notes//| |1| Make a new folder corresponding to the //`project name`//| | | |2||clic {key Create_project}, follow path to this folder {key Select_folder}|// it has to be an empty folder//| |3|`Copy` your images within this folder, by creating a subfolder `images`||// to be readable on several computers, the images have to be in a subfolder of the project folder//| |4||clic {key Add_images}, select images from the folder `images`|//you can add one, or several, image(s) at a time, more details in [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/import_vsi/ | 3. Import VSI]]//| ==Procedure to open a project== Now, everyone (with "reading" right to the destination folder) can access the images from every computer: # Start QuPath # Press {key Open_project} # Double-clic on the thumbnail image =3. Import VSI= First, you need to install the [[ https://github.com/qupath/qupath-bioformats-extension | BioFormats extension ]]. Then you can follow these [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/import_vsi/| instructions ]]. =4.Export annotations within QuPath= Using [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/export_annotations_groovy/| Groovy script]] works for 1 image or 1 project. Using [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/export_annotations_imagej/| ImageJ macro]] works for 1 image =5. Image Processing & Analysis = ==5.1 Color Deconvolution == === using QuPath === [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/define-stain-vectors/ |tutorial ]] === using ImageJ Plugin combined with Threshold == Using the ImageJ plugin through [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/color_decon_threshold/ | ImageJ macro]] == 5.2 Analyse by Annotations names == A Groovy [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/qps-analysis_by_annotationclasses/ | script ]] for QuPath