= 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`
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'
=== 1.1.b. Mac OSX ===
(WARNING) Get the compiled version at **smb://svfas6.epfl.ch/biop/public/0 - BIOP Data/0-Install/QuPath/QuPath MAC**
**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
(WARNING) The versions above contain all the extensions you need in the `Extensions` Subfolder
==1.2. QuPath Setup ==
=== 1.2.a. Directories ===
The BIOP has 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
=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 : ** \\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 }
{F8728917}
==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