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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Hi @haesleinhuepf , @Christian_Tischer, @aklemm, @schmiedc sorry for the delay in answering, Indeed we are trying to get the list of available training , http://biii.eu/all-content?type=book&field_type_target_id=All

BUT its exposition (display) and table is ugly (see for example http://biii.eu/pixels-microns) . We are working on it. However the main fields are defined even if not developped that much let us know if not clear enough here : https://github.com/NeuBIAS/bise/issues , and has be thought to be compatible with an ELIXIR initiative called TESS refering all training in general during a EuroBioimaging/ Elixir/ NEUBIAS Taggathon.
To add a new training (once again, the way it is displayed will change)
as a registered tagger, once logged in, add new content/ add Training Material . More training needs to be entered, so I would be very grateful if you can enter some of the links you have given (I will do it otherwise :slight_smile: ) .
In a few words the general Following info are required to describe a training (most of them are optional) :

  • Title

  • Synopsis ( Free text description of the training material purpose, (such as learning outcomes),
    the summary field can be used as a short description for teaser views.) ,

  • Tools used for training (list of sofwtare entries covered by this training e.g ImageJ or a particular list of Tools in it) ,

  • URL (where to dowload it, ideally a readme file listing the content in term of files available if not only a book , otherwise the upper level including data and code catch up.),

  • DOI if available: of the training material , not of the data set or code

  • Author(s)

  • Trainer(s) /Presenter(s) The person which presented the training material? Note: is it of interest only when links to an event. (Event field)

  • Date start date of the event where it was presented, or last modified date for the materia at the time of the curation.

  • Prerequisites : could also be seen as Target Audience. For example it can point to link to training material that would be recommended to follow first, or a usage level recommended.

  • Topics covered: Should be Edam bio imaging topics and operations , as suggested in the autocompletion. If you need to add other words, add them in the next field “Free topics” that will be considered for edam insertion then. Programming Language is also added here as a topic (to be discussed)

  • Format : Which format ? Book /Book chapter / workshop material / video tutorial (or webinar) / Tutorial (short explanation about specific topic) /web… It is a taxonomy for now, for which terms can be added in this test version.

  • Content Type : Components / Collections / Workflow / Language / General (i do not know for now in the taxonomy to be changed). We are not sure about the utility of it: it could as well infererd from the Tools used in this training (where a specific workflow should also be described as an entry in bise, and then refereed to)

  • Parent Previous referred training material on which this training material was built in. Use existing entries or a title if it does not exist in the registry of training material, this will create a new link that can then be completed afterwards with the link were to access it.

  • License: The name of the license indicating the rights for reuse/modification of this training material . If no license indicated, you can not use part of it.

  • Expected duration: Time needed to go trough this training, in hours. may be modified in the form by a proper duration field.

  • Then has slides, has practical exercices, has image dataset…

  • Additional keyworkds : tag you wanted to add for the topics but were not able to find

  • has executable: any docker image, binder site, jupiter link that can be used directly whatever the student computer configuration
    Next BIG UPDATE of the biii.eu site in October (maybe sooner for training exposition)
    Cheers,
    Perrine

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Hi Tischi,

I’ll also do some shameless self-advertisement. Here’s the link to a course I created to teach image processing with Python and Jupyter that covers a pretty wide range of topics:


Cheers,
Guillaume

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