Originally posted at forum.image.sc and even more originally tweeted here

QuPath v0.2.0-m3 is now online!

There are many changes, mostly below the surface - but quite a few above the surface too.

The biggest differences involve projects, which have been completely revised. It’s now easier to import images (just drag & drop multiple files) & QuPath tries harder to help resolve broken paths (e.g. when your images move).

Importing images Fixing URIs

You can finally set pixel sizes by double-clicking the values under the ‘Image’ tab - optionally with a line or area drawn to help figure out the calibration

Sidenote: you’ll need to be using a project to store the changes…

Setting pixels by area Setting pixels by line

A major reason to update projects was to add ‘fancy’ images in the future, which aren’t stored directly in a single file but might need to be calculated dynamically (e.g. by applying some kind of transform). This could be to crop regions, concatenate channels, normalize colors…

Create sparse image from project is a first example. It generates a new image consisting of regions extracted from other images in a project (all the ones with an annotation classified as ‘Region*’). I expect this to be useful one day… maybe to train a pixel classifier.

Sparse images

Speaking of which, the pixel classifier remains a work-in-progress. Not yet save-able or scriptable, it has been extensively revised & can calculate some new features (including some in 3D!) on its path to being useful.

Feature selection

Viewing features

New, perceptually uniform colormaps have also arrived (thanks go here):


Magma (I think)

There’s more control when you send images to ImageJ - including z-stacks

Sending to ImageJ

Bio-Formats v6.2.0 is included - which means improved WSI support thanks to the the Bio-Formats team & Glencoe Software. QuPath’s ability to write pyramidal OME-TIFF images is also much improved (albeit still mostly accessible by scripting).

Exporting OME-TIFF

The brush & wand are better. Previously, exuberant brushing would result in lots of disconnected circles - now things are smoother. Also, with a compatible graphics tablet the Wand is pressure sensitive - and both tools behave a better with touchscreens.

v0.2.0-m2 Brushing in m2

v0.2.0-m3 Brushing in m3

And lastly, especially for coders, there’s a first implementation of a GsonTools class to help convert various QuPath-related things to & from a JSON representation. Here, it’s applied to convert a QuPath object into a GeoJSON feature.