Bioimage Analysis: Recommended Reading and Viewing

Hi All,

@haesleinhuepf @simonfn @imagejan @Kota @apoliti @VolkerH @aklemm

Do you have recommendations for self-study material (“recommended reading” or “recommended viewing”) on Bioimage Analysis?

I currently have this modest list:

But I am sure I am missing a lot of relevant material…

Thanks!
Tischi

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Hey Tischi,

my list of favorites is a bit longer :stuck_out_tongue:

Dominic Waithes ONBI course:

Dave Masons online course:
http://pcwww.liv.ac.uk/~dnmason/reveal_ia/ImageAnalysisWithFiji.html

Dan Whites / IPF MPI CBG slides:



And how about Albert Cardonas Fiji scripting tutorial?
https://www.ini.uzh.ch/~acardona/fiji-tutorial/

Last but not least shameless self-advertising our online teaching material:

As far as I know the BISE should allow us entering teaching material at some point, but I haven’t heard news from @Kota and @PerrineGilloteaux about that. Maybe they can comment on the current state?

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Hi Tischi,

this is more or less what I know, too. Adding https://www.youtube.com/channel/UCmh81PBL4lU6r6mcGqhRPbQ/playlists
which is a collection of videos by Sonja Aits,
and
https://www.wiley.com/en-us/Standard+and+Super+Resolution+Bioimaging+Data+Analysis%3A+A+Primer-p-9781119096900
(have not read it, also it is not free)

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Hi @Christian_Tischer,

I think the book “Digital Image Processing: An Algorithmic Introduction Using Java” by Wilhelm Burger and Mark J. Burge is a good reference.
https://link.springer.com/book/10.1007%2F978-1-4471-6684-9

Cheers,
Mauro

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Yes BISE allows for tagging also training material.
Under Content Type: training material

Cheers,
Christopher

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Hi Tischi,

I would add Kota’s book from 2016 (new version coming soon):
https://www.imaging-git.com/news/now-available-download-open-access-textbook-bioimage-data-analysis-edited-kota-miura

Also, I found the first 2.5 chapters of Gonzalez and Woods’ Digital Image Processing helpful
http://www.imageprocessingplace.com

More mathematically oriented and very good: Bernd Jähne’s Digital Image Processing (there are pdfs to be found online)

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What is the target audience? If it is bio-image analysts wanting to deepen their knowledge of the algorithms I would also suggest Pierre Soille’s book, which is unfortunately out of print.

I second @simonfn regarding Bernd Jaehne’s book for the fundamentals (linear filters, point operations etc) - although some parts of it (classification etc) are meanwhile a bit outdated.

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