0.6 release notes #158

finglis · 2025-06-19T13:22:57Z

PR to update the 0.6 detailed release notes including updates to general docs sections greatly impacted by changes to features/UI related to:

QuPath Tour
Toolbar reorganisation (exceptions need to be made as its a very common pane)
Annotation names
Class pane
Measurement tables (exceptions also made as its a very common pane)
ImageJ + fiji running together - docs section, release notes section + images linked
ImageJ script runner - docs section, release notes + images linked
Multi-dimensional section?

finglis · 2025-06-19T13:23:31Z

Justification for the majority of "getting started" section images being updated is that they are mostly read by new users so its more important for the toolbar etc to represent what they also have on their screen. The screenshots themselves don't take long to do.

Also includes deletions of unused images, changing from jpg/png where incorrect. Images captured with system default as snapshot extension broke

petebankhead · 2025-06-23T11:10:12Z

docs/tutorials/multiplex_analysis.md

-:::{sidebar} Accurate cell detection
-Good cell segmentation is really *essential* for accurate multiplexed analysis.
-New and improved methods of segmenting cells in QuPath are being actively explored...
+:::{sidebar} Precise cell detection


I don't see a reason to change this, I think 'Accurate' more accurately describes what is intended here - https://en.wikipedia.org/wiki/Accuracy_and_precision

alanocallaghan · 2025-06-23T11:32:47Z

It feels like the release notes template shouldn't live on the main branch

Also, release notes needs to be in TOC

alanocallaghan · 2025-06-23T11:34:54Z

docs/reference/release_notes.md


 ## 🚀 Major features

-### New InstanSeg Segmentation
+### Extension Manager/Wrangler


I would drop "wrangler"

alanocallaghan · 2025-06-23T12:10:33Z

I updated the lonely instanseg dark mode screenshot and removed the semi-useless one showing the progress bar

petebankhead · 2025-06-23T14:33:30Z

@alanocallaghan Any reason not to make the screenshot JPEG? The PNG is big...

…-docs into 0.6-release-notes

alanocallaghan · 2025-06-23T14:54:52Z

No, I'd have just used the default options in the screenshot tool

…-docs into 0.6-release-notes

alanocallaghan · 2025-06-23T16:34:38Z

docs/reference/release_notes.md

 :class: shadow-image full-image

 InstanSeg segmentation of nuclei in a fluorescent image
 :::

-***TODO*** Update images once InstanSeg page is complete (since images have been compressed)
+### Major OMERO Extension Reset


Suggested change

### Major OMERO Extension Reset

### Major OMERO Extension Overhaul

alanocallaghan · 2025-06-23T16:35:12Z

docs/reference/release_notes.md

 :::

-:::{figure} https://global.discourse-cdn.com/business4/uploads/imagej/optimized/3X/a/9/a970374cfd08ec4708364ca5b42807ceaaa24133_2_690x392.jpeg
+### New InstanSeg Segmentation


### New InstanSeg Segmentation Method

or

### New InstanSeg Extension

...?

alanocallaghan · 2025-06-23T16:37:50Z

docs/reference/release_notes.md


-### OME-Zarr images are now supported
+The OMERO extension has been completely rewritten under the hood, improving it's flexibility and giving access to more features such as the ability to retrieve pixel values (including raw values) in the way that your server is set up.


Suggested change

The OMERO extension has been completely rewritten under the hood, improving it's flexibility and giving access to more features such as the ability to retrieve pixel values (including raw values) in the way that your server is set up.

The OMERO extension has been completely rewritten under the hood, improving its flexibility and giving access to more features.

It now allows you directly to retrieve raw pixel values using three different methods depending on how your extension and OMERO server are set up.

alanocallaghan · 2025-06-23T16:39:09Z

docs/reference/release_notes.md

-* **Got lots of things to select?** Quickly activate the selection tool by pressing 'S' when the main viewer is selected.
+### OME-Zarr images are now supported 🎉
+
+It's now possible to open and work with OME-Zarr images in QuPath! OME-Zarr was developed by the OME team in collaboration with many individuals and institutes with the goal to provide a more efficient and scalable format for large images. To get started using this file type in QuPath, drag and drop an OME-Zarr image into the main window or use the 'Open' dialog to select an OME-Zarr image. Alternatively, you can also export to OME-Zarr format.


Suggested change

It's now possible to open and work with OME-Zarr images in QuPath! OME-Zarr was developed by the OME team in collaboration with many individuals and institutes with the goal to provide a more efficient and scalable format for large images. To get started using this file type in QuPath, drag and drop an OME-Zarr image into the main window or use the 'Open' dialog to select an OME-Zarr image. Alternatively, you can also export to OME-Zarr format.

It's now possible to open and work with OME-Zarr images in QuPath!

OME-Zarr was developed by the OME team in collaboration with many individuals and institutes, with the goal to provide a more efficient and scalable format for large images.

To get started using this file type in QuPath, drag and drop an OME-Zarr image into the main window or use the 'Open' dialog to select an OME-Zarr image.

Alternatively, you can also export to OME-Zarr format.

alanocallaghan · 2025-06-23T16:39:20Z

docs/reference/release_notes.md


-### Viewing Annotation Names
+To learn more about OME-Zarr check out [this paper](https://link.springer.com/article/10.1007/s00418-023-02209-1) and how to export in QuPath [here](../advanced/exporting_images.html).


don't use [here] links

alanocallaghan · 2025-06-23T16:40:22Z

docs/reference/release_notes.md

-### Selection mode refresh
+Following on from the QuPath tour, you may of notice the toolbar is looking a little different from before.
+One new button has been added which allows for quick viewing of connections between objects (if you have any).
+Viewer related tools such as "show scalebar", "show grid" and "show input display" have been combined into a dropdown button so that these less frequently used tools aren't always on screen, making the toolbar less busy.


Suggested change

Viewer related tools such as "show scalebar", "show grid" and "show input display" have been combined into a dropdown button so that these less frequently used tools aren't always on screen, making the toolbar less busy.

Viewer related tools such as "Show scalebar", "Show grid" and "Show input display" have been combined into a dropdown button so that these less frequently used tools aren't always on screen, making the toolbar less busy.

These should also be guilabel if they're in the docs (although presumably not on image.sc)

I would be inclined to use backticks eg Show scalebar as it at least makes it visually distinct, but idk if that's suitable for GUI text

alanocallaghan · 2025-06-23T16:42:12Z

docs/reference/release_notes.md


-### Selection mode refresh
+Following on from the QuPath tour, you may of notice the toolbar is looking a little different from before.
+One new button has been added which allows for quick viewing of connections between objects (if you have any).


I think "(if you have any)" is redundant and a bit ambiguous? Could be objects or connections

alanocallaghan · 2025-06-23T16:42:47Z

docs/reference/release_notes.md


-***TODO***: Add images of log scaling once general doc update is complete
+Lastly, the selection mode can now be quickly accessed by using the 'S' key when the main viewer is selected.


Suggested change

Lastly, the selection mode can now be quickly accessed by using the 'S' key when the main viewer is selected.

Lastly, selection mode can now be quickly accessed by using the 'S' key when the main viewer is selected.

alanocallaghan · 2025-06-23T16:43:53Z

Sections should all be "Title Case" or "Sentence case" but not a mix (I prefer "Sentence case" for titles anyway...)

alanocallaghan · 2025-06-23T16:47:14Z

docs/reference/release_notes.md


-:::{Figure} https://github.com/user-attachments/assets/12d7060b-35bc-40ca-89a3-f837c5417dbf
-:class: mid-image
+Navigating through time series and z-stacks now features a refreshed visual design, aimed at making it easier to explore your images. Additionally, for those looking to get a general overview of the z-stack, a maximum intensity projection overlay can now be displayed on top of the image. To learn more about this, check out the [multidimensional image documentation](../advanced/multidimensional_images.md).


Suggested change

Navigating through time series and z-stacks now features a refreshed visual design, aimed at making it easier to explore your images. Additionally, for those looking to get a general overview of the z-stack, a maximum intensity projection overlay can now be displayed on top of the image. To learn more about this, check out the [multidimensional image documentation](../advanced/multidimensional_images.md).

Navigating through time series and z-stacks now features a refreshed visual design, aimed at making it easier to explore your images.

Additionally, for those looking to get a general overview of a z-stack, you can now display an overlay using various projections (e.g., maximum or mean intensity projection).

To learn more about this, check out the [multidimensional image documentation](../advanced/multidimensional_images.md).

alanocallaghan · 2025-06-23T16:50:48Z

docs/reference/release_notes.md


-## 🐛 Bugs fixed
+For those of you who use ImageJs macro language, this also can be used within QuPath. Although an existing QuPath feature, the ImageJ script runner has had a visual update and some under-the-hood improvements. To learn more about how to use this feature, check out the [ImageJ script runner documentation](../advanced/imagej.md#running-macros--scripts).


Suggested change

For those of you who use ImageJs macro language, this also can be used within QuPath. Although an existing QuPath feature, the ImageJ script runner has had a visual update and some under-the-hood improvements. To learn more about how to use this feature, check out the [ImageJ script runner documentation](../advanced/imagej.md#running-macros--scripts).

For those of you who use ImageJs macro language, good news!

QuPath 0.6.0 features a new and improved ImageJ script runner.

Now you have much more control over how data is sent to and received from ImageJ, as well as the ability to run both groovy scripts and ImageJ macros.

The legacy ImageJ macro runner is still around if you need it, though.

To learn more about how to use this feature, check out the [ImageJ script runner documentation](../advanced/imagej.md#running-macros--scripts).

alanocallaghan · 2025-06-23T16:52:17Z

docs/reference/release_notes.md

-### OME.tiff exporting 8 bit
-When using the Tile exporter to export an OME.tiff image, the image previously went through a RGB check that resulted in the images wrongly being converted to 8-bit.
-It now exports in the correct bit depth of the original image.
+### QuPath and fiji built together


Suggested change

### QuPath and fiji built together

### QuPath and Fiji built together

alanocallaghan · 2025-06-23T17:01:04Z

docs/reference/release_notes.md


-## 👩‍💻 Scripting and API changes
+!I may not be the best person to hype this up


Suggested change

!I may not be the best person to hype this up

While QuPath has long had ImageJ support, this was somewhat limited in only running in "original ImageJ mode", meaning there was limited support for Fiji plugins and no access to ImageJ2's new features.

Building QuPath and Fiji together unlocks some of these powerful new features and many extra plugins!

You can find out more on [Building from source](https://qupath.readthedocs.io/en/latest/docs/reference/building.html#building-with-fiji).

alanocallaghan · 2025-06-23T17:06:46Z

docs/reference/release_notes.md

-TMA cores now by default are assigned a specific class when created, keeping them further distinguished from other annotations types.
-The default color for this class is now lighter to make it easier to see for both brightfield and fluorescent images.
-If a core is missing from the grid then it will be displayed the same color as the other cores but with more transparency.
+Viewing the names of annotations has been tweaked to make it easier to see which label relates to which annotation, particularly when annotations are small or overlap with others. The label is now consistently displayed at the top of the annotation and better adjusts to objective changes.


Suggested change

Viewing the names of annotations has been tweaked to make it easier to see which label relates to which annotation, particularly when annotations are small or overlap with others. The label is now consistently displayed at the top of the annotation and better adjusts to objective changes.

Viewing the names of annotations has been tweaked to make it easier to see which label relates to which annotation, particularly when annotations are small or overlap with others.

The label is now consistently displayed at the top of the annotation and better adjusts to magnification changes.

alanocallaghan · 2025-06-23T17:08:50Z

docs/reference/release_notes.md

-:::{figure} https://global.discourse-cdn.com/business4/uploads/imagej/optimized/3X/a/9/a970374cfd08ec4708364ca5b42807ceaaa24133_2_690x392.jpeg
+### New InstanSeg Segmentation
+
+It's here!!! The award winning [InstanSeg](https://github.com/qupath/qupath-extension-instanseg) segmentation method from Thibaut Goldsborough you can now do so in QuPath via the InstanSeg extension. This extension provides a greatly improved accuracy in segmentation of cells for both brightfield and fluorescent images. It also gets increasingly speedy with GPU support. Learn more about InstanSeg and how to use it in QuPath [here](../deep/instanseg.md).


Suggested change

It's here!!! The award winning [InstanSeg](https://github.com/qupath/qupath-extension-instanseg) segmentation method from Thibaut Goldsborough you can now do so in QuPath via the InstanSeg extension. This extension provides a greatly improved accuracy in segmentation of cells for both brightfield and fluorescent images. It also gets increasingly speedy with GPU support. Learn more about InstanSeg and how to use it in QuPath [here](../deep/instanseg.md).

The award winning [InstanSeg](https://github.com/instanseg/instanseg) segmentation method from Thibaut Goldsborough can be used in QuPath via the [InstanSeg extension](https://github.com/qupath/qupath-extension-instanseg).

This extension provides greatly improved accuracy in segmentation of cells for both brightfield and fluorescent images.

It also gets increasingly speedy with GPU support.

Learn more about InstanSeg and how to use it in QuPath on [its page in the docs](../deep/instanseg.md).

finglis added 9 commits June 11, 2025 08:27

rework post call

b941db2

catalog

51daa3f

omero image

9d5e1c8

Lauras edits

6ae697e

Merge branch 'main' into 0.6-release-notes

4757212

started compilation

3121305

key measurement table update

e5f5c10

Merge branch '0.6-starting-out/tutorial-updates' into 0.6-release-notes

300fa82

linking images

af5a0f0

finglis added 2 commits June 19, 2025 16:55

Merge branch 'main' into 0.6-release-notes

24ace80

Suggestions, class list and measurement table updates

20dd996

Also includes deletions of unused images, changing from jpg/png where incorrect. Images captured with system default as snapshot extension broke

petebankhead reviewed Jun 23, 2025

View reviewed changes

alanocallaghan reviewed Jun 23, 2025

View reviewed changes

alanocallaghan added 2 commits June 23, 2025 12:58

Update some images and do some linting

db26e6d

png not jpg

2267d36

finglis added 2 commits June 23, 2025 15:35

imageJ

3502792

Merge branch '0.6-release-notes' of https://github.com/finglis/qupath…

e320ce1

…-docs into 0.6-release-notes

alanocallaghan and others added 3 commits June 23, 2025 16:08

Remove png

1e6edc8

updated cell detection annotation images

f034917

Merge branch '0.6-release-notes' of https://github.com/finglis/qupath…

ca26ebc

…-docs into 0.6-release-notes

alanocallaghan reviewed Jun 23, 2025

View reviewed changes

	### Major OMERO Extension Reset
	### Major OMERO Extension Overhaul


		### OME-Zarr images are now supported
		The OMERO extension has been completely rewritten under the hood, improving it's flexibility and giving access to more features such as the ability to retrieve pixel values (including raw values) in the way that your server is set up.

	The OMERO extension has been completely rewritten under the hood, improving it's flexibility and giving access to more features such as the ability to retrieve pixel values (including raw values) in the way that your server is set up.
	The OMERO extension has been completely rewritten under the hood, improving its flexibility and giving access to more features.
	It now allows you directly to retrieve raw pixel values using three different methods depending on how your extension and OMERO server are set up.


		### Viewing Annotation Names
		To learn more about OME-Zarr check out [this paper](https://link.springer.com/article/10.1007/s00418-023-02209-1) and how to export in QuPath [here](../advanced/exporting_images.html).

	Viewer related tools such as "show scalebar", "show grid" and "show input display" have been combined into a dropdown button so that these less frequently used tools aren't always on screen, making the toolbar less busy.
	Viewer related tools such as "Show scalebar", "Show grid" and "Show input display" have been combined into a dropdown button so that these less frequently used tools aren't always on screen, making the toolbar less busy.


		*TODO*: Add images of log scaling once general doc update is complete
		Lastly, the selection mode can now be quickly accessed by using the 'S' key when the main viewer is selected.

	Lastly, the selection mode can now be quickly accessed by using the 'S' key when the main viewer is selected.
	Lastly, selection mode can now be quickly accessed by using the 'S' key when the main viewer is selected.


		## 🐛 Bugs fixed
		For those of you who use ImageJs macro language, this also can be used within QuPath. Although an existing QuPath feature, the ImageJ script runner has had a visual update and some under-the-hood improvements. To learn more about how to use this feature, check out the [ImageJ script runner documentation](../advanced/imagej.md#running-macros--scripts).

-For those of you who use ImageJs macro language, this also can be used within QuPath. Although an existing QuPath feature, the ImageJ script runner has had a visual update and some under-the-hood improvements. To learn more about how to use this feature, check out the [ImageJ script runner documentation](../advanced/imagej.md#running-macros--scripts).
+For those of you who use ImageJs macro language, good news!
+QuPath 0.6.0 features a new and improved ImageJ script runner.
+Now you have much more control over how data is sent to and received from ImageJ, as well as the ability to run both groovy scripts and ImageJ macros.
+The legacy ImageJ macro runner is still around if you need it, though.
+To learn more about how to use this feature, check out the [ImageJ script runner documentation](../advanced/imagej.md#running-macros--scripts).

	### QuPath and fiji built together
	### QuPath and Fiji built together


		## 👩‍💻 Scripting and API changes
		!I may not be the best person to hype this up

-!I may not be the best person to hype this up
+While QuPath has long had ImageJ support, this was somewhat limited in only running in "original ImageJ mode", meaning there was limited support for Fiji plugins and no access to ImageJ2's new features.
+Building QuPath and Fiji together unlocks some of these powerful new features and many extra plugins!
+You can find out more on [Building from source](https://qupath.readthedocs.io/en/latest/docs/reference/building.html#building-with-fiji).

	Viewing the names of annotations has been tweaked to make it easier to see which label relates to which annotation, particularly when annotations are small or overlap with others. The label is now consistently displayed at the top of the annotation and better adjusts to objective changes.
	Viewing the names of annotations has been tweaked to make it easier to see which label relates to which annotation, particularly when annotations are small or overlap with others.
	The label is now consistently displayed at the top of the annotation and better adjusts to magnification changes.

-It's here!!! The award winning [InstanSeg](https://github.com/qupath/qupath-extension-instanseg) segmentation method from Thibaut Goldsborough you can now do so in QuPath via the InstanSeg extension. This extension provides a greatly improved accuracy in segmentation of cells for both brightfield and fluorescent images. It also gets increasingly speedy with GPU support. Learn more about InstanSeg and how to use it in QuPath [here](../deep/instanseg.md).
+The award winning [InstanSeg](https://github.com/instanseg/instanseg) segmentation method from Thibaut Goldsborough can be used in QuPath via the [InstanSeg extension](https://github.com/qupath/qupath-extension-instanseg).
+This extension provides greatly improved accuracy in segmentation of cells for both brightfield and fluorescent images.
+It also gets increasingly speedy with GPU support.
+Learn more about InstanSeg and how to use it in QuPath on [its page in the docs](../deep/instanseg.md).

0.6 release notes #158

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0.6 release notes #158

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