= 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 `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}
# Double-clic on the thumbnail image
=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 =
==5.1 Color Deconvolution and 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