Bioimage Analysis in FIJI – Resource List
Posted by Wilson Adams, 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.
- FIJI Download: https://fiji.sc
- Open Imaging Community Forum: https://forum.image.sc/ (also https://forum.microlist.org/)
- All of the ImageJ User Guides – https://imagej.net/User_Guides
- Scripting Commands: https://imagej.nih.gov/ij/developer/macro/functions.html
Online Slides:
- Dave Mason’s Slides on Image Analysis with FIJI: {I really like this one}
http://pcwww.liv.ac.uk/~cci/reveal_ia/ImageAnalysisWithFiji.html - Cool thread on using FFT to blend images from York and Prerbisch: https://twitter.com/AndrewGYork/status/1030153302464323585
Books
- Analyzing fluorescence microscopy images with ImageJ: https://petebankhead.gitbooks.io/imagej-intro/content/
- Bioimage Data Analysis Workflow: https://www.springer.com/gp/book/9783030223854
- Springer Image Processing Textbook: https://link.springer.com/content/pdf/10.1007%2F978-1-4471-6684-9.pdf
Video Courses:
- Robert Haase’s Bioimage Analysis Course: {I really like this one}
https://www.youtube.com/playlist?list=PL5ESQNfM5lc7SAMstEu082ivW4BDMvd0U - The whole NEUBIAS Youtube channel is a fantastic resource
https://www.youtube.com/channel/UC-oy7UpEhRfHQ-5ePCviKFg - Aits Lab Youtube Channel on Image Analysis tutorials: https://www.youtube.com/channel/UCmh81PBL4lU6r6mcGqhRPbQ/playlists
- FIJI Scripting Workshop: https://vimeo.com/218520432
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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There is also the RMS web database – https://www.rms.org.uk/discover-engage/online-microscopy-talks.html