Welcome! This website hopes to get you started with single-cell tracking, segmentation and visualization in organoids.
What are organoids?
Organoids are mini-organs that you can grow in the lab. The resemble the real organ, and show some of its functionality. For example, intestinal organoids resemble the intestines, and show the same cell types and roughly the same behavior.
Organoids have revolutionized many fields, and are nowadays an indispensable tool for basic research, where we observe how an organ functions, for disease modeling, where we investigate how a certain disease affects an organ, and for personalized medicine, where we use organoids made from patients to which treatment works best for that particular patient.
What knowledge is assumed?
Cell tracking in complex structures, like organoids, is still hard. So don’t expect quick results. Still, I’m convinced that any lab can set up automated organoid analysis, given that they have someone that is interested in computer stuff.
You need some basic programming skills. You need to know what variables and functions are, and what loops and if-statements are. If you don’t have that, I recommend working through chapters 1 to 11 of the book Automate the Boring Stuff with Python. It’s a very practical book (and free!), and teaches you the basics of programming using the Python programming language.
What do you provide?
See the main menu! This website is focused on tracking and segmenting cells in organoids. So if you want to know from microscopy images what each individual cell is doing, but you don’t know how to analyze those images, you’re at the right address.
Why did you create this website?
I see that more and more research groups are analyzing organoids at the single-cell level. Yet, the resources found online about this are scarce. That’s a shame. With this website, I hope to give you enough pointers so that you can successfully do research.
Who are you?
My name is Rutger, and I’m a researcher at the University Medical Center of Utrecht, working as a senior research analist in the lab of Maria RodrÃguez Colman. There, I study organoids, mostly computational stuff. Previously, I did a PhD at AMOLF, in the groups of Sander Tans and Jeroen van Zon, working on tracking down how intestinal organoids function.
Find me at:
You can reach me at rutger@rutgerkok.nl.