Bioimage Analysis in FIJI – Resource List

Posted by , on 14 September 2020

If you are on this site, you might be aware of some of the open source image processing and analysis tools are available to you. The toolbox in this space is rapidly expanding. But that doesn’t always mean it’s easy to navigate – it can actually be quite daunting. Luckily the bio-imaging community is friendly and helpful – there are now TONS of resources available to hit the ground running as a newcomer

Personally, as long as FIJI has been around, I have been evangelizing about it to my colleagues (I’m sure they’re sick of it). It has been extremely valuable for my research in so many ways. And even after nearly a decade, I’m still constantly learning about new things you can do with it.

By now, dozen’s of people have asked me to “teach them FIJI” by now – which is an ambitious request. For the sake of efficiency (and my sanity) I have resorted to pulling together an ever-growing list of resources that I have found helpful in learning and using FIJI over the last few years. Hopefully some of you may find it useful.

Disclaimer: It seems like there’s great new resources for FIJI popping up everyday. I do keep a list, and I’ll provide some follow-ups to this list in the future as it grows.

Online Slides:


Video Courses:

Beyond FIJI

Aside from the ecosystem within FIJI, there are so many useful image processing tools available for free with Python, Java, Octave, and so many more. These are largely outside my wheelhouse at the moment, but I’d encourage you to check out the Open Imaging Community Forum to see what other tools are out there that may be useful for your work.

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