From Zero to QuPath Hero – A journey unveiled

Hello FocalPlane readers! I’m Laura, a postdoc researcher in biomedical image analysis and artificial intelligence. My journey in this field began with my PhD at Universidad Carlos III, in Madrid, where I focused on developing novel tools for colour analysis and image registration in microscopy. When I finished my thesis, I wanted to find a position where I could be actively helpful in improving how we view and analyze images, but preferably somewhere I wouldn’t melt during the summer months. And so, in June 2023, I joined the team developing QuPath,  an open-source software for bioimage analysis. QuPath offers efficient, rigorously tested image analysis features while also allowing you to create your own extensions and plugins. Moreover, it fosters a vibrant collaborative, training, and educational community. I was particularly drawn to this team because of its commitment to accessibility and innovation, making it an ideal environment to contribute my expertise and continue pushing the boundaries of biomedical image analysis. 

What if we could embrace this shared experience of failure while learning?

Despite my dedication to research, I face challenges due to chronic illness. There are times when my body refuses to cooperate with what I would wish to do, and instead forces me to lie down and rest. While frustrating, being forced to slow down and stop checking emails, downloading papers, and fixing code bugs, liberates my head and allows me to think freely and imaginatively about new projects and ideas. During one of these moments, I found myself pondering what contributions I could offer to QuPath. The new team already boasted with great programmers, UX/UI experts, masters of pathology and biostatistics… While I am competent in algorithm creation, my recent struggles with background segmentation had left me slightly tired of coding and on top of that, I was seriously missing lecturing and being able to be a bit more creative with my own material. And while we had been talking about organising QuPath workshops, I questioned how I could teach something in which I wasn’t proficient, since my knowledge of the software could only be described as shallow. The answer became clear—I had to become an expert in QuPath. Yet, the prospect seemed daunting. Every time I have to learn something from scratch, I tend to become so frustrated that quitting is dangerously tempting. Then it occurred to me—I could not be alone in feeling this way. Surely, many others, especially those with advanced expertise in their fields, also grappled with learning new things from scratch, facing failures they hadn’t encountered before. What if we could embrace this shared experience of failure while learning? Inspired by this idea, I decided to document my journey of learning QuPath from scratch, creating tutorials where mistakes happen, and the learning process isn’t always smooth and perfect.  

I shared the idea with Pete, and he liked it. Not only would it be good for me and future QuPath newbies, but it would help find problematic bits in the user experience that fail to be reported because new users will often assume they are the ones doing things wrong. I got green light, now I needed to figure out how to execute it. I needed to make it engaging enough that no one would lose motivation half-way through (specially me). I had been listening to a lot of Greek mythology books and thought it would be fun to shape the experiment as a Hero’s Journey, thus the name: From Zero to QuPath Hero. The general structure of a Hero’s Journey has been repeated throughout history: an individual, living quietly is shocked by an unexpected incident that makes them consider their future and, with the help of a mentor, start training to undertake successively difficult obstacles. As their adventure progresses, the mentor is left behind (dead or no longer helpful) and the challenges become increasingly dangerous, to the point where the Hero must make friends or allies to overcome them, until finally they succeed in their final quest and are able to return home as a wise ruler or now mentor.  

I wanted our video series to intricately mirror this structure, and so I started to plan and divide the series into different stages:  

1. The Call to Action: We embark on a journey initiated by a mentor figure – the docs, symbolizing guidance into the unknown realm of QuPath. We introduce our vlogging series as an invitation to all who have contemplated delving into QuPath but have hesitated due to its perceived complexity. We entice them with the promise of a comprehensive pipeline they can learn to construct independently, setting the stage for an adventure of discovery and growth.  

2. Trials of Worth: We encounter obstacles while following the guidance of the “docs”, gradually improving our skills and confidence through overcoming challenges, fostering a sense of shared frustration and progress among viewers. 

3. The First Threshold: A significant milestone is achieved as we complete an entire image analysis pipeline independently, marking a shift from reliance on external guidance to self-reliance and deeper understanding. 

4. Into the Maw: The journey intensifies as we delve into more complex challenges, such as learning scripting and programming, requiring us to seek assistance beyond traditional means and engage with community forums for support. 

5. The Supreme Ordeal: We reach a transformation point where scripting proficiency allows us to tackle larger challenges, crafting our own solutions and asserting autonomy through small projects like custom measurements and image overlays. 

6. Unification: Mastery nears as we undertake ambitious projects like creating a full QuPath extension, possibly requiring group collaboration, synthesizing our knowledge into significant achievements. 

7. Freedom to Live: Having conquered QuPath, we emerge triumphant, equipped with newfound skills and confidence, ready to explore new digital landscapes and potentially mentor others, becoming QuPath heroes. 

So far, we have had (mostly) smooth sailing through steps 1 and 2 and are eager to continue our journey. We really hope that viewers are enjoying it and that more people will join us. However, the best thing about this series is that it will be a lasting and accessible documentation on most (if not all) QuPath secrets. 

If you want to join us, check out the video series here and Twitter, where I announce all new uploads. Any level is welcome, from beginners to regular users who want to help and answer questions. Or maybe you are a regular user with a very specific question? You’ll be welcome too! Other members of the QuPath team are participating as well, giving solutions to the problems I (or you) may encounter along the way. Moreover, I will also be writing a post here every time I upload a new video, going through the process, the problems I encountered, and offering yet another way of creating a useful conversation around learning. We hope to see you being part of the journey! 

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