As v0.2.0-m6 is near, it’s time for another update on what’s going on & what’s planned.

Firstly, the big news is that QuPath has been selected as one of 42 projects to be funded by the Chan Zuckerberg Initiative under the Essential Open Source Software for Science program.

Alongside recent ISSF3 funding (University of Edinburgh/Wellcome Trust), things are looking rather a lot better in terms of supporting and developing the software, at least over the next 12 months or so.

Look out for more announcements in this regard… and perhaps also a QuPath workshop in 2020.

Meanwhile, back in 2019 the milestones continue. I appreciate that semi-frequent-but-somewhat-sporadic not-called-stable updates aren’t ideal and can be disruptive, but it has been a necessary consequence of me scrabbling around trying to find spare hours to write the code whenever I could.

Coding late

However, there would have been far fewer of those coding hours were it not for the irrepressible superuser Research Associate answering many of the questions on https://forum.image.sc/.

Along with Sara & Zbigniew from the La Jolla Institute for Immunology, RA has also been testing the latest milestones ahead of their release - helping to catch bugs almost as quickly as I have created them. So huge thanks to them!

I do hope that, despite disruption, the milestone approach has been useful. I have found it helpful (albeit stressful…) to get feedback as it went along, rather than coding in isolation for a year and then turning up suddenly with a whole new version no one wants.

It also seemed to me practically necessary, because supporting the old stuff while my head is full of the new stuff I’m currently working on is… hard.

Although supporting a plethora of milestone versions is also hard. If you are stuck on an older milestone, please do think of updating… at least for your next project, and do check out the changelog with each new release to see if there have been any bugs fixed that might affect you.

I hope to get off the milestone track over the next few months - and then start on the next version.

To demystify the process and help with planning, here’s my todo list for v0.2.0, describing the things that I think are essential before it can be considered stable:

1. Refining existing features

  • Polishing up the pixel classifier.
    • Improving the options for scripting, converting to objects and making measurements.
  • Rewriting the object classifier
    • Bringing it more in line with the pixel classifier.
    • Improve support for more complex classification (e.g. with multiplexed images)

2. Documentation

  • User documentation
    • An all-new website that is more comprehensive and more maintainable.
  • Developer documentation
    • Comprehensive javadocs hosted… somewhere.

3. Performance & stability

  • Handling more objects
    • Continuous improvements in how to work with & query large numbers of objects.
  • Better progress monitoring
    • Is it working? Has it crashed? Ideally QuPath would give more feedback & not leave us guessing.
  • Fixing bugs

There is a lot more I would like to include. But I think these three main topics are the most urgent, and the most useful to the most people.

There will certainly be more to come later. I hope the brighter funding outlook will help QuPath transition into becoming a more wholeheartedly community project, and less subject to the whims (and mistakes) of a single developer.

To that end, I’d ask that if you are using the software and care about where it goes, please get involved!

The software really shouldn’t be seen as something that just exists and sometimes changes, but rather something you can actively help shape and influence.

One way is through participating in image.sc - not solely to ask questions, but also to answer them and take part in wider discussions.

I suggest the forum first because I prefer to keep things public where possible, so that the discussions might help others as well. However, if you want to talk projects and collaborations where the forum isn’t a good fit and I should wear my academic hat, you can also find me at the University of Edinburgh.

In the end, QuPath is just a tool that is hopefully useful. My interest is in trying to apply image analysis to further biomedical research - and hope that QuPath can help meet some of the needs in this area.