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).
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…
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.
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.
New, perceptually uniform colormaps have also arrived (thanks go here):
There’s more control when you send images to ImageJ - including z-stacks
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).
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.
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.
And while I’m here, if you want to help make QuPath better, faster, join me in Edinburgh!
There’s a Research Fellow position currently being advertised (deadline 8 August).
Note: If you prefer to receive this information in tweet form, it’s at https://twitter.com/QuPath/status/1153748322471088128