= 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` (NOTE) or dowload and extract [[https://drive.google.com/a/epfl.ch/file/d/1YtXdABBV0G9VrvllMWhAH057s3Uy_SOz/view?usp=sharing | the zip archive ]] 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** (NOTE) or dowload and extract [[https://drive.google.com/a/epfl.ch/file/d/1TuaOHpw_8YdudImf33ql_oP-6G2CPXfX/view?usp=sharing | the zip archive ]] **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\** to your favorite location and run `QuPath.exe` (NOTE) or dowload and extract [[https://drive.google.com/a/epfl.ch/file/d/1YtXdABBV0G9VrvllMWhAH057s3Uy_SOz/view?usp=sharing | the zip archive ]] 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`) as shown in 1.2.a. === 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** (NOTE) or dowload and extract [[https://drive.google.com/a/epfl.ch/file/d/1TuaOHpw_8YdudImf33ql_oP-6G2CPXfX/view?usp=sharing | the zip archive ]] **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\** to your favorite location and run `QuPath.exe` (NOTE) or dowload and extract [[https://drive.google.com/a/epfl.ch/file/d/1YtXdABBV0G9VrvllMWhAH057s3Uy_SOz/view?usp=sharing | the zip archive ]] 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`) as shown in 1.2.a. === 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** (NOTE) or dowload and extract [[https://drive.google.com/a/epfl.ch/file/d/1TuaOHpw_8YdudImf33ql_oP-6G2CPXfX/view?usp=sharing | the zip archive ]] **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