= Documentation =
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) .
==1.1. QuPath Latest Versions ==
The BIOP is maintaining the current version with the latest bugfixes for
===1.1.a. Win 10 ===
(NOTE) Just "Copy & Paste" the folder **\\svfas6.epfl.ch\biop\public\0 - BIOP Data\0-Install\QuPath\0.1.3-SNAPSHOT** to your favorite location and run `QuPath.exe`
=== 1.1.b. Mac OSX ===
(WARNING) Get the compiled version at **smb://svfas6.epfl.ch/biop/public/0 - BIOP Data/0-Install/QuPath/0.1.3-SNAPSHOT MAC**
==1.2. Extensions ==
===1.2.a. BIOP's computer===
If you have trouble opening VSI file, go to {nav Edit > Preferences > Extensions Directory }
Select C:\QuPath_extensions\
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===1.2.b. Your computer===
Download the Extensions
Drag and drop the jar file on QuPath window and choose where to install the extension
=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 =
(IMPORTANT) On our server : **[[ file://///svfas6.epfl.ch/biop/public/0%20-%20BIOP%20Data/Scripts%20QuPath/ | \\svfas6.epfl.ch\biop\public\0 - BIOP Data\Scripts QuPath\ ]]** ,
You can find some **//"useful"//** scripts
(NOTE) You can make this folder YOUR Default Scripts folder , by setting it into {nav Edit > Preferences > Script Directory }
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==5.1 Color Deconvolution ==
=== using QuPath ===
[[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/define-stain-vectors/ |tutorial ]]
=== using ImageJ Plugin combined with 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