In this post, Charlie Farley from the OER services talks to Dr Bankhead about the process of creating and publishing his open textbook, managing copyright issues, student feedback and impact, and advice for those considering creating open textbooks. Dr Peter Bankhead is a Reader at the Institute of Genetics and Cancer↗️ and creator of digital imaging open-source software, QuPath↗️. This post belongs to Learning & Teaching Enhancement theme: Open Textbooks↗️.
Charlie Farley : Could you share with our readers who you are and how you came to create an open textbook?
Peter Bankhead: I’m a Reader in the Institute of Genetics and Cancer at The University of Edinburgh. My first degree was in Divinity, and then I changed direction and studied for a MSc in Computer Science and a PhD in Biomedical Sciences. I thought my PhD would involve building on biology with lab work and analysis, but it ended up being 100% analysis. As I hadn’t been taught image analysis before, it was difficult learning the key ideas quickly – and applying them at a PhD level. Because of this I really empathise with the biologists and biomedical scientists I meet who find themselves needing to learn how to analyse their imaging data, which requires quite different skills from what they were trained in.
During my first postdoc, I found myself needing to explain concepts to biologists who – like me – hadn’t been trained in image analysis. So, I started to create new training resources. The initial handbook that I wrote was a big 195-page PDF online, and when people started wanting to re-use it, I realised that I didn’t know the rules around this myself. My experiences with making software open had taught me that sharing doesn’t just mean putting something online, but also being clear with licenses. I ended up completely revising the content of the PDF and replacing many of the images. It feels better that it can now be used by other people and by my future self, no matter where I am.
Charlie Farley: What was your process in deciding where to host and publish your open textbook?
Peter Bankhead: After updating the PDF I added the the documentation to GitHub and published using GitBook. I also use Jupyter Book – also open-source – which makes the book interactive. For example, the figures created using Python code can be modified so learners can see how the figure changes. This gives an extra level to use the book to explore new image processing concepts.
Charlie Farley: You said that you went through a process of checking the copyright of everything that you used in there and replacing images. How did you find that process?
Peter Bankhead : Oh, torturous! There are images that are widely used among researchers and instructors, but it’s difficult to find 100% clear statements on their licensing. And there were microscopy images I’d used that didn’t have explicit agreement for sharing under open license – because I hadn’t realised at the time how important that would become. Which meant I had to remove these and find replacements.
I know I’m not alone in this. At a workshop I connected with another attendee about how we both found ourselves recreating our materials during the pandemic. He had the idea of submitting an opinion paper about why people should share training resources under clear open licences, which we’ve just done. Sharing training resources is important not just for learners, but for other trainers: we can create better and more advanced resources if we don’t need to continually spend time reinventing what already exists from scratch.
Charlie Farley: What sort of feedback have you gotten from students and colleagues and peers?
Peter Bankhead: Every now and again I meet someone working in the field, and they tell me that they first encountered image analysis through my book. That’s always encouraging! I also hear from people working in the field that the book is one that they recommend to their students.
One exciting thing happening now is that Beth Cimini from the Centre for Open Bioimage Analysis in the US, is starting to translate bioimage analysis resources into different languages and they’ve chosen this book as one of their first. We have a machine translation in Spanish and German – now we need native speakers to edit and improve this.
Charlie Farley: The last question I want to ask you is what would you say to somebody who is thinking about creating an open textbook?
Peter Bankhead: If the alternative is to create a closed textbook, I would say create an open textbook! I’ve certainly found it rewarding. I was much more motivated to work on it because I knew that it had the potential to help more people than something closed and restricted. I’ve learned a lot as the book has evolved over the years, and it has helped with the in-person workshops I’ve taught along the way. I understand the topics better because I’ve spent a long time thinking about how to explain them and benefited from others’ feedback.
It also opens a lot of doors – it can end up creating new opportunities you could never expect, both for yourself and for others.
PETER BANKHEAD
Dr Peter Bankhead↗️, is a Reader at the Institute of Genetics and Cancer, The University of Edinburgh. Creator of digital imaging open-source software, QuPath↗️, which has been downloaded close to half a million times, cited in about 3,000 academic articles, and is used all over the world, both in academia and industry. Dr Bankhead has published his open textbook Introduction to Bioimage Analysis↗️ using GitHub↗️ and Jupyter Books↗️.
STEPHANIE (CHARLIE) FARLEY
Stephanie (Charlie) Farley provides support and training in the creation and use of OER across the University and maintains the Open.Ed↗️ webpages.
Charlie works closely with the Geoscience Outreach↗️ course organisers and students to facilitate the student creation of OERs in collaboration with local schools and community groups. View the OEGlobal award winning collection of student made OERs on our TES repository: University of Edinburgh’s Open.Ed Open Educational Resources on TES↗️
Additionally, Charlie leads the 23 Things for Digital Knowledge↗️ programme, and the ISG Playful Engagement↗️ themes and goals.
