= 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. See Section 1.2.a. on how to set your **Extensions ** folder from within QuPath (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

This page contains information on how to setup QuPath 0.3 and how to migrate 0.2 to 0.3 scripts and protocols = Installing QuPath = Install the latest version of QuPath from https://qupath.github.io/ = BIOP Installation = You can copy the "QuPath Common Data" folder from ``` WIN: \\svraw1\ptbiop\public\0-Software\QuPath MAC: smb://svraw1/ptbiop/public\0-Software\QuPath ``` or download the[[ https://drive.google.com/file/d/1fz7P41CTqkcHKT91lVdjRtNDCqJLft4D/view?usp=sharing | ZIP from the BIOP GDrive ]] (~14Mb) Place the `QuPath Common Data` folder somewher permanent on your computer 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 Extensions> Installed Extensions} and locate `BIOP QuPath Extension` {F22627804, 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\biop-scripts` {F15226503, 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` = Installing StarDist for QuPath = [[ https://github.com/qupath/qupath-extension-stardist | StarDist now exists as a QuPath Extension ]], and on a fresh QuPath install, all you need to do is drag and drop the release JAR into QuPath. This will copy it into the `extensions` directory. Otherwise it is included in `QuPath Common Data` which can be downloaded here: `\\svraw1\ptbiop\public\0-Software\QuPath` = Migrating StarDist Models = StarDist models now need to be in `*.pb` format as per [[ https://github.com/qupath/qupath-extension-stardist#converting-a-tensorflow-model-for-use-with-opencv | this note by Pete Bankhead on the StarDist Extension Repo ]] == Install a Virtual Environment for the conversion == Pip Dependencies: {F21324420} **If you use `venv` with `py` and want to install in `D:\env-tf2onnx`** ``` py -3.7 -m venv d:\env-tf2onnx d:\env-tf2onnx\Scripts\activate\ pip install -r tf2onnx.txt ``` **If you use `conda`** ``` conda create -n env-tf2onnx python=3.7 conda activate env-tf2onnx pip install -r tf2onnx.txt ``` == Converting a Model from a StarDist Training == 1. Locate the resulting **model folder **from StarDist training (not the ZIP file). The example here assumes it is called `demo-model` 2. Run the following command ``` python -m tf2onnx.convert --opset 10 --saved-model "L:\public\0-BIOP_Data\StarDist Models\demo-model" --output_frozen_graph "L:\public\0-BIOP_Data\StarDist Models\demo-model.pb" ``` 3. This creates a single file `demo-model.pb` 4. Point to this file in the new StarDist Extension from within QuPath

= Documentation =This page contains information on how to setup QuPath 0.3 and how to migrate 0.2 to 0.3 scripts and protocols = Installing QuPath = Install the latest version of QuPath from https://qupath.github.io/ = BIOP Installation = You can copy the "QuPath Common Data" folder from 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 .``` WIN: \\svraw1\ptbiop\public\0-Software\QuPath MAC: smb://svraw1/ptbiop/public\0-Software\QuPath ``` or download the[[ https://drive.google.com/file/d/1fz7P41CTqkcHKT91lVdjRtNDCqJLft4D/view?usp=sharing | ZIP from the BIOP GDrive ]] (~14Mb) = Presentation =Place the `QuPath Common Data` folder somewher permanent on your computer [[ https://docs.google.com/presentation/d/1OmBUK-_2Ex66Wn3cYxInxzfadOVAcDp_gbSm7m9nKN4/edit?usp=sharing | Google Slides ]] (accessible to all EPFL users) =12. From QuPath, go to {nav Edit > Preferences...} 3. Install = ==1.1.Under {nav Extensions > QuPath user directory} point to the previously copied `QuPath Common Data` {F14241650, layout=center, QuPath Latest Versions == The BIOP is maintaining the current version with the latest in house bugfixes for ===1.1.asize=full} 4. Restart QuPath 5. Win 10 ===Go to {nav Extensions> Installed Extensions} and locate `BIOP QuPath Extension` (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`{F22627804, layout=center, size=full} (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,== Common Scripts == To have BIOP scripts (and your own) available for any open QuPath Project, you need to set the `Script directory` 1. use "Map network drive" on windows and use your GASPAR login but add 'intranet\' before your login name: 'intranet\username' ** Extensions for Windows **Go to {nav Edit > Preferences > Automation} After you start the new version of 2. Set the `Script directory` to`QuPath go toCommon Data\biop-scripts` {nav Edit > Preferences} and find **Extensions Directory for windows ** Set it to the `extensions` directory inside your QuPath folder.F15226503, layout=center, (e.g. `C:\QuPath\extensions`) as shown in 1.2.a. === 1.1.bsize=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. Mac OSX ===Go go {nav Edit > Preferences > ImageJ} and set the `ImageJ plugins directory` (we set is a subfolder of `QuPath Common Data`) (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**{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` - 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= Installing StarDist for QuPath = [[ https://github.com/qupath/qupath-extension-stardist | StarDist now exists as a QuPath Extension ]], and on a fresh QuPath install, all you need to do is drag and drop the release JAR into QuPath. This will copy it into the `extensions` directory. - Setup the Extensions folder within QuPath as per the paragraph below to wherever you copied the **Extensions** folder. See Section 1.2.a. on how to set your **Extensions ** folder from within QuPathOtherwise it is included in `QuPath Common Data` which can be downloaded here: `\\svraw1\ptbiop\public\0-Software\QuPath` (WARNING) The versions above contain all the extensions you need in the `Extensions` Subfolder= Migrating StarDist Models = ==1.2. QuPath Setup ==StarDist models now need to be in `*.pb` format as per [[ https://github.com/qupath/qupath-extension-stardist#converting-a-tensorflow-model-for-use-with-opencv | this note by Pete Bankhead on the StarDist Extension Repo ]] === 1.2.a. Directories === Computers at== Install a Virtual Environment for the BIOP have the QuPath directories set as follows:conversion == Pip Dependencies: {F21324420} From QuPath, go to {nav Edit > Preferences }**If you use `venv` with `py` and set the followind directory fields by double clicking on themwant to install in `D:\env-tf2onnx`** - Extensions Directory: `C:\QuPath\extensions` {F9985762, size=full} =2. Create a project= ==Description==``` py -3.7 -m venv d:\env-tf2onnx d:\env-tf2onnx\Scripts\activate\ pip install -r tf2onnx.txt 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`**If you use `conda`** ``` # Create a folder called `Images` inside `QP-Project-Demo` and move all your images thereconda create -n env-tf2onnx python=3.7 # From QuPath, select {nav Creconda activate Project} and navigate to `QP-Project-Demo`env-tf2onnx pip install -r tf2onnx.txt # 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==== Converting a Model from a StarDist Training == 1. Locate the resulting **model folder **from StarDist training (not the ZIP file). The example here assumes it is called `demo-model` 2. Run the following command Now, everyone (with "reading" right to the destination folder) can access the images from every computer:``` # Start QuPathpython -m tf2onnx.convert --opset 10 --saved-model "L:\public\0-BIOP_Data\StarDist Models\demo-model" --output_frozen_graph "L:\public\0-BIOP_Data\StarDist Models\demo-model.pb" # Press {key Open_project},``` 3. select your **qpproj**This creates a single file and press {key Open} # Double-clic o`demo-model.pb` 4. Point to this file in the thumbnail image you want to visualizenew StarDist Extension from within QuPath