Change Details

= 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 . = Presentation = [[ https://docs.google.com/presentation/d/1OmBUK-_2Ex66Wn3cYxInxzfadOVAcDp_gbSm7m9nKN4/edit?usp=sharing | Google Slides ]] (accessible to all EPFL users) =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` NB: to connect to svfas6.epfl.ch, use "Map network drive" on windows and use your GASPAR login but add 'intranet\' before your login name: 'intranet\username' === 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 . = Presentation = [[ https://docs.google.com/presentation/d/1OmBUK-_2Ex66Wn3cYxInxzfadOVAcDp_gbSm7m9nKN4/edit?usp=sharing | Google Slides ]] (accessible to all EPFL users) =1. Install = ==1.1. QuPath Latest Versions == The BIOP is maintaining the current version with the latest in house bugfixes for ===1.1.a. Win 10 === (NOTE) Just "Copy & Paste" the QuPath folder located at **\\svfas6.epfl.ch\biop\public\0 - BIOP Data\0-Install\QuPath\** to your favorite location and run `QuPath.exe` NB: to connect to svfas6.epfl.ch, use "Map network drive" on windows and use your GASPAR login but add 'intranet\' before your login name: 'intranet\username' ** Extensions for Windows ** After you start the new version of QuPath go to {nav Edit > Preferences} and find **Extensions Directory for windows ** Set it to the `extensions` directory inside your QuPath folder. (e.g. `C:\QuPath\extensions`) === 1.1.b. Mac OSX === (NOTE) Get the compiled version at **smb://svfas6.epfl.ch/biop/public/0 - BIOP Data/0-Install/QuPath/QuPath MAC** **Extensions for Mac** - You will need to get the extensions at **smb://svfas6.epfl.ch/biop/public/0 - BIOP Data/0-Install/QuPath/Extensions** - Copy these in a folder - Setup the Extensions folder within QuPath as per the paragraph below to wherever you copied the **Extensions** folder (WARNING) The versions above contain all the extensions you need in the `Extensions` Subfolder ==1.2. QuPath Setup == === 1.2.a. Directories === Computers at the BIOP have the QuPath directories set as follows: From QuPath, go to {nav Edit > Preferences } and set the followind directory fields by double clicking on them - Extensions Directory: `C:\QuPath\extensions` {F9985762, size=full} =2. Create a project= ==Description== For images of a Project to be accessible from different computers they have to be **within the project folder**. == To create a QuPath project == # Create a folder that will contain the project, let's call it `QP-Project-Demo` # Create a folder called `Images` inside `QP-Project-Demo` and move all your images there # From QuPath, select {nav Create Project} and navigate to `QP-Project-Demo` # Click on {nav Add images} and select all the images you want to add to the project form the `Images` folder # Your Project is ready Specific details for VSI files can be found at [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/import_vsi/ | this Wiki Page]] ==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

= 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 . = Presentation = [[ https://docs.google.com/presentation/d/1OmBUK-_2Ex66Wn3cYxInxzfadOVAcDp_gbSm7m9nKN4/edit?usp=sharing | Google Slides ]] (accessible to all EPFL users) =1. Install = ==1.1. QuPath Latest Versions == The BIOP is maintaining the current version with the latest in house bugfixes for ===1.1.a. Win 10 === (NOTE) Just "Copy & Paste" the QuPath folder located at **\\svfas6.epfl.ch\biop\public\0 - BIOP Data\0-Install\QuPath\QuPath 0.1.3-SNAPSHOT** to your favorite location and run `QuPath.exe` NB: to connect to svfas6.epfl.ch, use "Map network drive" on windows and use your GASPAR login but add 'intranet\' before your login name: 'intranet\username' === 1.1.b. Mac OSX ===** Extensions for Windows ** (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===After you start the new version of QuPath go to 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{nav Edit > Preferences} and find **Extensions Directory for windows ** 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 =2Set it to the `extensions` directory inside your QuPath folder. (e.g. Create a project=`C:\QuPath\extensions`) ==Description===== 1.1.b. Mac OSX === 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!(NOTE) Get the compiled version at **smb://svfas6.epfl.ch/biop/public/0 - BIOP Data/0-Install/QuPath/QuPath MAC** **Extensions for Mac** ==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`//| | |- You will need to get the extensions at **smb://svfas6.epfl.ch/biop/public/0 - BIOP Data/0-Install/QuPath/Extensions** |2||clic {key Create_project}, follow path to this folder {key Select_folder}|// it has to be an empty- Copy these in a 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]]//|- Setup the Extensions folder within QuPath as per the paragraph below to wherever you copied the **Extensions** folder (WARNING) The versions above contain all the extensions you need in the `Extensions` Subfolder ==Procedure to open a project== Now,==1.2. QuPath Setup == === 1.2.a. everyone (with "reading" right to the destination folder) can access the images from every computer:Directories === # StartComputers at the BIOP have the QuPath directories set as follows: # Press {key Open_project}From QuPath, select your **qpproj** file and press {key Open}go to {nav Edit > Preferences } and set the followind directory fields by double clicking on them # Double-clic on the thumbnail image you want to visualize- Extensions Directory: `C:\QuPath\extensions` =3.{F9985762, Import VSI= First,size=full} =2. you need to install the [[ https://github.com/qupath/qupath-bioformats-extension | BioFormats extension ]].Create a project= 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===Description== For images of a Project to be accessible from different computers they have to be **within the project folder**. 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.== To create a QuPath project == Using [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/export_annotations_imagej/| ImageJ macro]] works for 1 image =5.# Create a folder that will contain the project, 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 }let's call it `QP-Project-Demo` # Create a folder called `Images` inside `QP-Project-Demo` and move all your images there # From QuPath, select {nav Create Project} and navigate to `QP-Project-Demo` # Click on {nav Add images} and select all the images you want to add to the project form the `Images` folder {F8728917}# Your Project is ready ==5.1 Color Deconvolution == === using QuPath =Specific details for VSI files can be found at [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/import_vsi/ | this Wiki Page]] ==Procedure to open a project== [[ 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 QuPathNow, 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