= 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]]