Phriction Projects Wikis Bioimaging And Optics Platform Image Processing QuPath History Version 42 vs 43
Version 42 vs 43
Version 42 vs 43
Content Changes
Content Changes
= 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`
(NOTE) or dowload and extract [[https://drive.google.com/a/epfl.ch/file/d/1YtXdABBV0G9VrvllMWhAH057s3Uy_SOz/view?usp=sharing | the zip archive ]]
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'
** Extensions for Windows **
After you start the new version of QuPath go to
{nav Edit > Preferences} and find
**Extensions Directory for windows **
Set it to the `extensions` directory inside your QuPath folder. (e.g. `C:\QuPath\extensions`) as shown in 1.2.a.
=== 1.1.b. Mac OSX ===
(NOTE) Get the compiled version at **smb://svfas6.epfl.ch/biop/public/0 - BIOP Data/0-Install/QuPath/QuPath MAC**
(NOTE) or dowload and extract [[https://drive.google.com/a/epfl.ch/file/d/1TuaOHpw_8YdudImf33ql_oP-6G2CPXfX/view?usp=sharing | the zip archive ]]
**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. See Section 1.2.a. on how to set your **Extensions ** folder from within QuPath
(WARNING) The versions above contain all the extensions you need in the `Extensions` Subfolder
==1.2. QuPath Setup ==
=== 1.2.a. Directories ===
Computers at the BIOP have 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
= 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`
(NOTE) or dowload and extract [[https://drive.google.com/a/epfl.ch/file/d/1YtXdABBV0G9VrvllMWhAH057s3Uy_SOz/view?usp=sharing | the zip archive ]]
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'
** Extensions for Windows **
After you start the new version of QuPath go to
{nav Edit > Preferences} and find
**Extensions Directory for windows **
Set it to the `extensions` directory inside your QuPath folder. (e.g. `C:\QuPath\extensions`) as shown in 1.2.a.
=== 1.1.b. Mac OSX ===
(NOTE) Get the compiled version at **smb://svfas6.epfl.ch/biop/public/0 - BIOP Data/0-Install/QuPath/QuPath MAC**
(NOTE) or dowload and extract [[https://drive.google.com/a/epfl.ch/file/d/1TuaOHpw_8YdudImf33ql_oP-6G2CPXfX/view?usp=sharing | the zip archive ]]
**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. See Section 1.2.a. on how to set your **Extensions ** folder from within QuPath
(WARNING) The versions above contain all the extensions you need in the `Extensions` Subfolder
==1.2. QuPath Setup ==
=== 1.2.a. Directories ===
Computers at the BIOP have 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
= 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`
(NOTE) or dowload and extract [[https://drive.google.com/a/epfl.ch/file/d/1YtXdABBV0G9VrvllMWhAH057s3Uy_SOz/view?usp=sharing | the zip archive ]]
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'
** Extensions for Windows **
After you start the new version of QuPath go to
{nav Edit > Preferences} and find
**Extensions Directory for windows **
Set it to the `extensions` directory inside your QuPath folder. (e.g. `C:\QuPath\extensions`) as shown in 1.2.a.
=== 1.1.b. Mac OSX ===
(NOTE) Get the compiled version at **smb://svfas6.epfl.ch/biop/public/0 - BIOP Data/0-Install/QuPath/QuPath MAC**
(NOTE) or dowload and extract [[https://drive.google.com/a/epfl.ch/file/d/1TuaOHpw_8YdudImf33ql_oP-6G2CPXfX/view?usp=sharing | the zip archive ]]
**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. See Section 1.2.a. on how to set your **Extensions ** folder from within QuPath
(WARNING) The versions above contain all the extensions you need in the `Extensions` Subfolder
==1.2. QuPath Setup ==
=== 1.2.a. Directories ===
Computers at the BIOP have 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
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