Phriction Projects Wikis Bioimaging And Optics Platform Image Processing QuPath History Version 36 vs 37
Version 36 vs 37
Version 36 vs 37
Edits
Edits
- Edit by romainGuiet, Version 37
- Oct 4 2018 10:39
- Edit by romainGuiet, Version 36
- Oct 4 2018 10:37
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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)
<iframe src="https://docs.google.com/presentation/d/e/2PACX-1vQKOcupt0u7E98D8T6aAFaXldFvJ-oJD2jovVO_Y9DwuBgW-cGINHLa60-kXGmSfNSJBnE_WttSs-Fk/embed?start=true&loop=false&delayms=60000" frameborder="0" width="800" height="460" allowfullscreen="true" mozallowfullscreen="true" webkitallowfullscreen="true"></iframe>
=1. Install =
==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\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/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\
{F8718004}
===1.2.b. Your computer===
Download the Extensions
Drag and drop the jar file (from the folder **\\svfas6.epfl.ch\biop\public\0 - BIOP Data\0-Install\QuPath\Extensions for 0.1.3 SNAPSHOT**) 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}, 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
= 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 bugfixes for
===1.1.a. Win 10 ===
(NOTE) Just "Copy & Paste" the folder **\\svfas6.epfl.ch\biop\public\0 - BIOP Data\0-Install\QuPath\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/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\
{F8718004}
===1.2.b. Your computer===
Download the Extensions
Drag and drop the jar file (from the folder **\\svfas6.epfl.ch\biop\public\0 - BIOP Data\0-Install\QuPath\Extensions for 0.1.3 SNAPSHOT**) 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}, 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
= 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)
<iframe src="https://docs.google.com/presentation/d/e/2PACX-1vQKOcupt0u7E98D8T6aAFaXldFvJ-oJD2jovVO_Y9DwuBgW-cGINHLa60-kXGmSfNSJBnE_WttSs-Fk/embed?start=true&loop=false&delayms=60000" frameborder="0" width="800" height="460" allowfullscreen="true" mozallowfullscreen="true" webkitallowfullscreen="true"></iframe>
=1. Install =
==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\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/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\
{F8718004}
===1.2.b. Your computer===
Download the Extensions
Drag and drop the jar file (from the folder **\\svfas6.epfl.ch\biop\public\0 - BIOP Data\0-Install\QuPath\Extensions for 0.1.3 SNAPSHOT**) 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}, 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
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