= Documentaion = You can find all the [[ https://github.com/qupath/qupath/wiki/ | documentation ]] on-line. =1. Install = [[https://github.com/qupath/qupath/releases/ | Download the latest release]] corresponding to your operating system ( Windows / OSX / Linux) and [[ https://github.com/qupath/qupath/wiki/Extensions | add some extensions ]], at least the [[ https://github.com/qupath/qupath-bioformats-extension | BioFormats extension ]] (you have 2 files to download and to Drag&Drop on QuPath window) . =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 `Raw_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 `Raw_images`|//you can add one, or several, image(s) at a time//| ==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.Open VSI files == First, you need to install the [[ https://github.com/qupath/qupath-bioformats-extension | BioFormats extension ]]. If you still have some issue, there is a known "bug" due to the pyramidal images sizes. Peter Bankhead make a groovy script to overcome (temporarly the problem - should be fixed in a next release) - add you images into the project - Dowload the `AlternativeBioformatsServer.groovy` file {F760685} - Drag&Drop the `groovy` file on QuPath - {nav Run > type=instructions, name=Run For Project} - Select all the images using {key >>} - Press {key Ok} Now if you Double-clic on the thumbnail image, the magic should happen ! =4.Export annotations within QuPath= [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/export_annotations_imagej/| ... using ImageJ macro for QuPath ]] [[ TBD | ... using Groovy script for QuPath ]]

= Documentaion = You can find all the [[ https://github.com/qupath/qupath/wiki/ | documentation ]] on-line. =1. Install = [[https://github.com/qupath/qupath/releases/ | Download the latest release]] corresponding to your operating system ( Windows / OSX / Linux) and [[ https://github.com/qupath/qupath/wiki/Extensions | add some extensions ]], at least the [[ https://github.com/qupath/qupath-bioformats-extension | BioFormats extension ]] (you have 2 files to download and to Drag&Drop on QuPath window) . =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 `Raw_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 `Raw_images`|//you can add one, or several, image(s) at a time//| ==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.Open VSI files == First, you need to install the [[ https://github.com/qupath/qupath-bioformats-extension | BioFormats extension ]]. If you still have some issue, there is a known "bug" due to the pyramidal images sizes. Peter Bankhead make a groovy script to overcome (temporarly the problem - should be fixed in a next release) - add you images into the project - Dowload the `AlternativeBioformatsServer.groovy` file {F760685} - Drag&Drop the `groovy` file on QuPath - {nav Run > type=instructions, name=Run For Project} - Select all the images using {key >>} - Press {key Ok} Now if you Double-clic on the thumbnail image, the magic should happen ! =4.Export annotations within QuPath= [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/export_annotations_imagej/| ... using ImageJ macro]] [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/export_annotations_groovy/| ... using Groovy script]]

= Documentaion = You can find all the [[ https://github.com/qupath/qupath/wiki/ | documentation ]] on-line. =1. Install = [[https://github.com/qupath/qupath/releases/ | Download the latest release]] corresponding to your operating system ( Windows / OSX / Linux) and [[ https://github.com/qupath/qupath/wiki/Extensions | add some extensions ]], at least the [[ https://github.com/qupath/qupath-bioformats-extension | BioFormats extension ]] (you have 2 files to download and to Drag&Drop on QuPath window) . =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 `Raw_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 `Raw_images`|//you can add one, or several, image(s) at a time//| ==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.Open VSI files == First, you need to install the [[ https://github.com/qupath/qupath-bioformats-extension | BioFormats extension ]]. If you still have some issue, there is a known "bug" due to the pyramidal images sizes. Peter Bankhead make a groovy script to overcome (temporarly the problem - should be fixed in a next release) - add you images into the project - Dowload the `AlternativeBioformatsServer.groovy` file {F760685} - Drag&Drop the `groovy` file on QuPath - {nav Run > type=instructions, name=Run For Project} - Select all the images using {key >>} - Press {key Ok} Now if you Double-clic on the thumbnail image, the magic should happen ! =4.Export annotations within QuPath= [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/export_annotations_imagej/| ... using ImageJ macro for QuPath ]] [[ TBD | ... using Groovy script for QuPath https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/export_annotations_groovy/| ... using Groovy script]]