Change Details

This page contains information and protocols related to the latest version of QuPath (v0.2.1 as of July 2020) IMPORTANT: The **BIOP** recommends that you update to the latest QuPath and migrate your older projects to the new version. Please request assistance migrating scripts to our image analysts or sign up for our [[ mailto:olivier.burri@epfl.ch?subject=QuPath Migration Help | QuPath Migration sessions ]] = [[ mailto:olivier.burri@epfl.ch?subject=QuPath Migration Help |QuPath Migration Sessions]] = If people are registered, these sessions will take place **Every Wednesday at 13h30** and last about 1h. == Topics Covered == 1. Installation of the new QuPath version 2. Migrating QuPath v0.1.2-v0.1.4 to the latest version 3. Overview of changes and QA NOTE: We **will not** use these sessions to migrate your code from QuPath v0.1.4. Please book an appointment with the script's creator as necessary. = Installing QuPath 0.2.0 = As opposed to previous versions, the BIOP is now keeping in sync with the official releases of QuPath found here https://qupath.github.io/ We will always be working with the **'Latest Stable Release'** == Installing the BIOP-Extensions == 0. Go to `\\svfas6\biop\public\0 - BIOP Data\0-Install\QuPath` 1. Copy the `QuPath Common Data` directory to a location (We copy it directly to `C:\`) 2. From QuPath, go to {nav Edit > Preferences...} 3. Under {nav Extensions > QuPath user directory} point to the previously copied `QuPath Common Data` {F14241650, layout=center, size=full} 4. Restart QuPath 5. Go to {nav Help > Installed Extensions} and locate `BIOP Scripting Extensions` {F14241660, layout=center, size=full} == Common Scripts == To have BIOP scripts (and your own) available for any open QuPath Project, you need to set the `Script directory` 1. Go to {nav Edit > Preferences > Automation} 2. Set the `Script directory` to`QuPath Common Data\scripts` {F14241747, layout=center, size=full} == Extra Plugins and ImageJ Plugins == If you need a plugin from Fiji-ImageJ that will be run either manually within QuPath's ImageJ or with a script using a `run(...)` command, you need to **copy the jar file to the `ImageJ plugins directory` **. 1. Go go {nav Edit > Preferences > ImageJ} and set the `ImageJ plugins directory` (we set is a subfolder of `QuPath Common Data`) {F14241693, layout=center, size=full} NOTE: If you are going to run this code within a script **using the API directly**, you need to copy it to `QuPath Common Data\extensions` == Native StarDist Support == QuPath 0.2.0 includes a native way to run StarDist which is documented here: https://qupath.readthedocs.io/en/latest/docs/advanced/stardist.html WARNING: As stated in the documentation, this is an **Experimental Extension** that will change in the future. This requires the installation of a TensorFlow-enabled QuPath which has to be built on your machine and for which no direct download exists. The BIOP provides a compiled version for Windows on ` \\svfas6\biop\public\0 - BIOP Data\0-Install\QuPath` called **QuPath-0.2.1-TF** NOTE: As we do not have macOS systems available for building QuPath, we can help you get a Mac version running through a collaboration = Importing Older QuPath Projects = Older projects need to be migrated to a new project. All data is kept. 1. Create a new folder for the updated project 2. Drag and Drop that folder into QuPath, Click yes when prompted to create a new Project 3. See below: == Relative Paths == If your project had relative paths ( If `{PROJECT_DIR}` appears when you open your `project.qpproj` file with Notepad), you can use the script {nav Automate > User Scripts > Import old QuPath project with relative paths} == Absolute Paths == If your project has absolute paths, then you can use {nav File > Project... > Import images from v0.1.2} At the end of this process, if everything worked, your new project folder will contain all the annotations and results from before and the *absolute paths to your images** = Images, Changes with the latest QuPath = The latest version of QuPath **does not support relative paths** for your images. This means that the new strategy consists in 1. Storing your raw images somewhere (You lab share, Locally, etc..) 2. Creating your QuPath project folder somewhere (Can be the same location, or your 'Analysis' folder) 3. Load the images into QuPath == Problems and Solutions with Absolute Paths == One advantage is that all your experimental data can reside in the same place, with the QuPath projects being elsewhere, which facilitates - Sharing of QuPath projects among collaborators: If someone edits the QuPath project, they can send the Zipped folder to their colleagues. As the folder no longer contains the images, it is quite small. - Storing your raw data somewhere, and your analysis elsewhere, decoupling QuPath from the raw data. That way you can store all raw data (Not just the QuPath raw data in the same location, which can help you get organized) NOTE: However this means that when you or someone else opens the new QuPath Project, **the absolute location of the images might be different** QuPath will announce that it cannot find the image data after you open the project {F14241822, layout=center, size=full} You can use {nav Search...} to locate once again the folder containing the images and QuPath will update the location of all the images {F14241828, layout=center, size=full} After you click {nav Apply changes}, the project is updated and you can again navigate === Limitations === If you are loading images from multiple locations, this will most likely not work. If you wish to sort images for a project, make sure they are all in a common folder (Subfolders are OK)

This page contains information and protocols related to the latest version of QuPath (v0.2.1 as of July 2020) IMPORTANT: The **BIOP** recommends that you update to the latest QuPath and migrate your older projects to the new version. Please request assistance migrating scripts to our image analysts or sign up for our [[ mailto:olivier.burri@epfl.ch?subject=QuPath Migration Help | QuPath Migration sessions ]] = [[ mailto:olivier.burri@epfl.ch?subject=QuPath Migration Help |QuPath Migration Sessions]] = If people are registered, these sessions will take place **Every Wednesday at 13h30** and last about 1h. == Topics Covered == 1. Installation of the new QuPath version 2. Migrating QuPath v0.1.2-v0.1.4 to the latest version 3. Overview of changes and QA NOTE: We **will not** use these sessions to migrate your code from QuPath v0.1.4. Please book an appointment with the script's creator as necessary. = Installing QuPath 0.2.0 = As opposed to previous versions, the BIOP is now keeping in sync with the official releases of QuPath found here https://qupath.github.io/ We will always be working with the **'Latest Stable Release'** == Common Scripts == To have BIOP scripts (and your own) available for any open QuPath Project, you need to set the `Script directory` 1. Go to {nav Edit > Preferences > Automation} 2. Set the `Script directory` to`QuPath Common Data\scripts` {F14241747, layout=center, size=full} == Installing the BIOP-Extensions == 0. Go to `\\svfas6\biop\public\0 - BIOP Data\0-Install\QuPath` 1. Copy the `QuPath Common Data` directory to a location (We copy it directly to `C:\`) 2. From QuPath, go to {nav Edit > Preferences...} 3. Under {nav Extensions > QuPath user directory} point to the previously copied `QuPath Common Data` {F14241650, layout=center, size=full} 4. Restart QuPath 5. Go to {nav Help > Installed Extensions} and locate `BIOP Scripting Extensions` {F14241660, layout=center, size=full} == Extra Plugins and ImageJ Plugins == If you need a plugin from Fiji-ImageJ that will be run either manually within QuPath's ImageJ or with a script using a `run(...)` command, you need to **copy the jar file to the `ImageJ plugins directory` **. 1. Go go {nav Edit > Preferences > ImageJ} and set the `ImageJ plugins directory` (we set is a subfolder of `QuPath Common Data`) {F14241693, layout=center, size=full} 2. Restart QuPath NOTE: If you are going to run this code within a script **using the API directly**, you need to copy it to `QuPath Common Data\extensions` == Native StarDist Support == QuPath 0.2.0 includes a native way to run StarDist which is documented here: https://qupath.readthedocs.io/en/latest/docs/advanced/stardist.html WARNING: As stated in the documentation, this is an **Experimental Extension** that will change in the future. This requires the installation of a TensorFlow-enabled QuPath which has to be built on your machine and for which no direct download exists. The BIOP provides a compiled version for Windows on ` \\svfas6\biop\public\0 - BIOP Data\0-Install\QuPath` called **QuPath-0.2.1-TF** NOTE: As we do not have macOS systems available for building QuPath, we can help you get a Mac version running through a collaboration = Importing Older QuPath Projects = Older projects need to be migrated to a new project. All data is kept. 1. Create a new folder for the updated project 2. Drag and Drop that folder into QuPath, Click yes when prompted to create a new Project 3. See below: == Relative Paths == If your project had relative paths ( If `{PROJECT_DIR}` appears when you open your `project.qpproj` file with Notepad), you can use the script {nav Automate > User Scripts > Import old QuPath project with relative paths} == Absolute Paths == If your project has absolute paths, then you can use {nav File > Project... > Import images from v0.1.2} At the end of this process, if everything worked, your new project folder will contain all the annotations and results from before and the *absolute paths to your images** = Images, Changes with the latest QuPath = The latest version of QuPath **does not support relative paths** for your images. This means that the new strategy consists in 1. Storing your raw images somewhere (You lab share, Locally, etc..) 2. Creating your QuPath project folder somewhere (Can be the same location, or your 'Analysis' folder) 3. Load the images into QuPath == Problems and Solutions with Absolute Paths == One advantage is that all your experimental data can reside in the same place, with the QuPath projects being elsewhere, which facilitates - Sharing of QuPath projects among collaborators: If someone edits the QuPath project, they can send the Zipped folder to their colleagues. As the folder no longer contains the images, it is quite small. - Storing your raw data somewhere, and your analysis elsewhere, decoupling QuPath from the raw data. That way you can store all raw data (Not just the QuPath raw data in the same location, which can help you get organized) NOTE: However this means that when you or someone else opens the new QuPath Project, **the absolute location of the images might be different** QuPath will announce that it cannot find the image data after you open the project {F14241822, layout=center, size=full} You can use {nav Search...} to locate once again the folder containing the images and QuPath will update the location of all the images {F14241828, layout=center, size=full} After you click {nav Apply changes}, the project is updated and you can again navigate === Limitations === If you are loading images from multiple locations, this will most likely not work. If you wish to sort images for a project, make sure they are all in a common folder (Subfolders are OK)

This page contains information and protocols related to the latest version of QuPath (v0.2.1 as of July 2020) IMPORTANT: The **BIOP** recommends that you update to the latest QuPath and migrate your older projects to the new version. Please request assistance migrating scripts to our image analysts or sign up for our [[ mailto:olivier.burri@epfl.ch?subject=QuPath Migration Help | QuPath Migration sessions ]] = [[ mailto:olivier.burri@epfl.ch?subject=QuPath Migration Help |QuPath Migration Sessions]] = If people are registered, these sessions will take place **Every Wednesday at 13h30** and last about 1h. == Topics Covered == 1. Installation of the new QuPath version 2. Migrating QuPath v0.1.2-v0.1.4 to the latest version 3. Overview of changes and QA NOTE: We **will not** use these sessions to migrate your code from QuPath v0.1.4. Please book an appointment with the script's creator as necessary. = Installing QuPath 0.2.0 = As opposed to previous versions, the BIOP is now keeping in sync with the official releases of QuPath found here https://qupath.github.io/ We will always be working with the **'Latest Stable Release'** == Installing th== Common Scripts == To have BIOP-Extensions == 0. scripts (and your own) available for any open QuPath Project, Go to `\\svfas6\biop\public\0 - BIOP Data\0-Install\QuPath`you need to set the `Script directory` 1. Copy the `QuPath Common Data` directory to a location (We copy it directly to `C:\`)Go to {nav Edit > Preferences > Automation} 2. From QuPath, go to {nav Edit > Preferences...}Set the `Script directory` to`QuPath Common Data\scripts` 3. Under {nav Extensions > QuPath user directory} point to the previously copied `QuPath Common Data` {F14241650747, layout=center, size=full} 4 == Installing the BIOP-Extensions == 0. Restart Go to `\\svfas6\biop\public\0 - BIOP Data\0-Install\QuPath` 51. Go to {nav Help > Installed Extensions} andCopy the `QuPath Common Data` directory to a locate `BIOP Scripting Extensions`ion (We copy it directly to `C:\`) {F142416602. From QuPath, layout=center,go to {nav Edit > Preferences...} 3. size=full} == Common Scripts == To have BIOP scripts (and your own) available for any open QuPath ProjectUnder {nav Extensions > QuPath user directory} point to the previously copied `QuPath Common Data` {F14241650, layout=center, you need to set the `Script directory`size=full} 14. Go to {nav Edit > Preferences > Automation}Restart QuPath 25. Set the `Script directory` to`QuPath Common Data\sGo to {nav Help > Installed Extensions} and locate `BIOP Scripts`ting Extensions` {F14241747660, layout=center, size=full} == Extra Plugins and ImageJ Plugins == If you need a plugin from Fiji-ImageJ that will be run either manually within QuPath's ImageJ or with a script using a `run(...)` command, you need to **copy the jar file to the `ImageJ plugins directory` **. 1. Go go {nav Edit > Preferences > ImageJ} and set the `ImageJ plugins directory` (we set is a subfolder of `QuPath Common Data`) {F14241693, layout=center, size=full} 2. Restart QuPath NOTE: If you are going to run this code within a script **using the API directly**, you need to copy it to `QuPath Common Data\extensions` == Native StarDist Support == QuPath 0.2.0 includes a native way to run StarDist which is documented here: https://qupath.readthedocs.io/en/latest/docs/advanced/stardist.html WARNING: As stated in the documentation, this is an **Experimental Extension** that will change in the future. This requires the installation of a TensorFlow-enabled QuPath which has to be built on your machine and for which no direct download exists. The BIOP provides a compiled version for Windows on ` \\svfas6\biop\public\0 - BIOP Data\0-Install\QuPath` called **QuPath-0.2.1-TF** NOTE: As we do not have macOS systems available for building QuPath, we can help you get a Mac version running through a collaboration = Importing Older QuPath Projects = Older projects need to be migrated to a new project. All data is kept. 1. Create a new folder for the updated project 2. Drag and Drop that folder into QuPath, Click yes when prompted to create a new Project 3. See below: == Relative Paths == If your project had relative paths ( If `{PROJECT_DIR}` appears when you open your `project.qpproj` file with Notepad), you can use the script {nav Automate > User Scripts > Import old QuPath project with relative paths} == Absolute Paths == If your project has absolute paths, then you can use {nav File > Project... > Import images from v0.1.2} At the end of this process, if everything worked, your new project folder will contain all the annotations and results from before and the *absolute paths to your images** = Images, Changes with the latest QuPath = The latest version of QuPath **does not support relative paths** for your images. This means that the new strategy consists in 1. Storing your raw images somewhere (You lab share, Locally, etc..) 2. Creating your QuPath project folder somewhere (Can be the same location, or your 'Analysis' folder) 3. Load the images into QuPath == Problems and Solutions with Absolute Paths == One advantage is that all your experimental data can reside in the same place, with the QuPath projects being elsewhere, which facilitates - Sharing of QuPath projects among collaborators: If someone edits the QuPath project, they can send the Zipped folder to their colleagues. As the folder no longer contains the images, it is quite small. - Storing your raw data somewhere, and your analysis elsewhere, decoupling QuPath from the raw data. That way you can store all raw data (Not just the QuPath raw data in the same location, which can help you get organized) NOTE: However this means that when you or someone else opens the new QuPath Project, **the absolute location of the images might be different** QuPath will announce that it cannot find the image data after you open the project {F14241822, layout=center, size=full} You can use {nav Search...} to locate once again the folder containing the images and QuPath will update the location of all the images {F14241828, layout=center, size=full} After you click {nav Apply changes}, the project is updated and you can again navigate === Limitations === If you are loading images from multiple locations, this will most likely not work. If you wish to sort images for a project, make sure they are all in a common folder (Subfolders are OK)