= Documentation = You can find all the [[ https://github.com/qupath/qupath/wiki/ | documentation ]] on-line, and some [[ https://www.youtube.com/playlist?list=PL4ta8RxZklWkPB_pwW-ZDVAGPGktAlE5Y | video tutorials ]] on youtube . =1. Install = ==1.1. QuPath Latest Versions == The BIOP is maintaining the current version with the latest bugfixes for ===1.1.a. Win 10 === (NOTE) Just "Copy & Paste" the folder **\\svfas6.epfl.ch\biop\public\0 - BIOP Data\0-Install\QuPath\QuPath 0.1.3-SNAPSHOT** to your favorite location and run `QuPath.exe` === 1.1.b. Mac OSX === (WARNING) Get the compiled version at **smb://svfas6.epfl.ch/biop/public/0 - BIOP Data/0-Install/QuPath/QuPath 0.1.3-SNAPSHOT MAC** ==1.2. Extensions == ===1.2.a. BIOP's computer=== If you have trouble opening VSI file, go to {nav Edit > Preferences > Extensions Directory } Select C:\QuPath_extensions\ {F8718004} ===1.2.b. Your computer=== Download the Extensions Drag and drop the jar file (from the folder **\\svfas6.epfl.ch\biop\public\0 - BIOP Data\0-Install\QuPath\Extensions for 0.1.3 SNAPSHOT**) on QuPath window and choose where to install the extension =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 = (IMPORTANT) On our server : ** \\svfas6.epfl.ch\biop\public\0 - BIOP Data\Scripts QuPath\ ** , You can find some **//"useful"//** scripts (NOTE) You can make this folder YOUR Default Scripts folder , by setting it into {nav Edit > Preferences > Script Directory } {F8728917} ==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

= Documentation = You can find all the [[ https://github.com/qupath/qupath/wiki/ | documentation ]] on-line, and some [[ https://www.youtube.com/playlist?list=PL4ta8RxZklWkPB_pwW-ZDVAGPGktAlE5Y | video tutorials ]] on youtube . =1. Install = ==1.1. QuPath Latest Versions == The BIOP is maintaining the current version with the latest bugfixes for ===1.1.a. Win 10 === (NOTE) Just "Copy & Paste" the folder **\\svfas6.epfl.ch\biop\public\0 - BIOP Data\0-Install\QuPath\QuPath 0.1.3-SNAPSHOT** to your favorite location and run `QuPath.exe` === 1.1.b. Mac OSX === (WARNING) Get the compiled version at **smb://svfas6.epfl.ch/biop/public/0 - BIOP Data/0-Install/QuPath/QuPath 0.1.3-SNAPSHOT MAC** ==1.2. Extensions == ===1.2.a. BIOP's computer=== If you have trouble opening VSI file, go to {nav Edit > Preferences > Extensions Directory } Select C:\QuPath_extensions\ {F8718004} ===1.2.b. Your computer=== Download the Extensions Drag and drop the jar file (from the folder **\\svfas6.epfl.ch\biop\public\0 - BIOP Data\0-Install\QuPath\Extensions for 0.1.3 SNAPSHOT**) on QuPath window and choose where to install the extension =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}, select your **qpproj** file and press {key Open} # Double-clic on the thumbnail image you want to visualize =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 = (IMPORTANT) On our server : ** \\svfas6.epfl.ch\biop\public\0 - BIOP Data\Scripts QuPath\ ** , You can find some **//"useful"//** scripts (NOTE) You can make this folder YOUR Default Scripts folder , by setting it into {nav Edit > Preferences > Script Directory } {F8728917} ==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

= Documentation = You can find all the [[ https://github.com/qupath/qupath/wiki/ | documentation ]] on-line, and some [[ https://www.youtube.com/playlist?list=PL4ta8RxZklWkPB_pwW-ZDVAGPGktAlE5Y | video tutorials ]] on youtube . =1. Install = ==1.1. QuPath Latest Versions == The BIOP is maintaining the current version with the latest bugfixes for ===1.1.a. Win 10 === (NOTE) Just "Copy & Paste" the folder **\\svfas6.epfl.ch\biop\public\0 - BIOP Data\0-Install\QuPath\QuPath 0.1.3-SNAPSHOT** to your favorite location and run `QuPath.exe` === 1.1.b. Mac OSX === (WARNING) Get the compiled version at **smb://svfas6.epfl.ch/biop/public/0 - BIOP Data/0-Install/QuPath/QuPath 0.1.3-SNAPSHOT MAC** ==1.2. Extensions == ===1.2.a. BIOP's computer=== If you have trouble opening VSI file, go to {nav Edit > Preferences > Extensions Directory } Select C:\QuPath_extensions\ {F8718004} ===1.2.b. Your computer=== Download the Extensions Drag and drop the jar file (from the folder **\\svfas6.epfl.ch\biop\public\0 - BIOP Data\0-Install\QuPath\Extensions for 0.1.3 SNAPSHOT**) on QuPath window and choose where to install the extension =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}, select your **qpproj** file and press {key Open} # Double-clic on the thumbnail image you want to visualize =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 = (IMPORTANT) On our server : ** \\svfas6.epfl.ch\biop\public\0 - BIOP Data\Scripts QuPath\ ** , You can find some **//"useful"//** scripts (NOTE) You can make this folder YOUR Default Scripts folder , by setting it into {nav Edit > Preferences > Script Directory } {F8728917} ==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