Image Processing and Analysis Glossary of Terms

Dear all on this forum.

@romainGuiet, @NicoKiaru, @seitz and I were wondering if anyone here had a link or a resource that they used as a reference for all the image processing and analysis terms we use.

1. Is there such a thing already available?

We’ve seen multiple web resources here and there with some glossary terms, but nothing really complete (or at least it was always missing one or two terms)

2. If it does not exist, would building such a page on the ImageJ.net wiki make sense?

We could start it by entering the terms we are using in our Image Processing And Analysis for Life Scientists MOOC, and have that page be expandable by the community. But of course we wouldn’t want to reinvent the wheel if there’s already a valid resource out there.

Your thoughts are welcome, especially our beloved @team

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Hey @oburri,

I think there are quite some books available with a lot of definitions of terms. My favorite editor Thomas Lehmann (Deserno)

https://link.springer.com/content/pdf/10.1007%2F978-3-642-15816-2.pdf

There are also some book-like online resources such as:
https://homepages.inf.ed.ac.uk/rbf/HIPR2/welcome.htm
https://homepages.inf.ed.ac.uk/rbf/HIPR2/index.htm

I’m not sure if copying things to imagej.net makes a lot of sense, as maintaining this information is additional workload… But collecting links to good resources might make sense :slight_smile:

Cheers,
Robert

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See, for example:
http://homepages.inf.ed.ac.uk/rbf/CVDICT/cvdict.htm

I think building (or leveraging, if a comprehensive effort is already underway) a glossary makes total sense. I would not do it on imagej.net, because it is not an ImageJ-specific project.

Possible ways forward:

  • I’ve been thinking we may need a new more general wiki for scientific image processing and analysis, something like wiki.image.sc. It is possible to use Discourse as a community-powered wiki. Imagine if every topic tagged with wiki, and/or in a Wiki category, automatically appeared at wiki.image.sc with proper navigation. I had intended to make a dedicated topic about this for discussion, but it’s relevant here, so may as well mention it. <gush>Even more amazing would be to recast all imagej.net pages as Discourse topics here tagged with imagej and wiki—friendlier than MediaWiki to edit, and probably powerful enough if we can sort out the navigation issues! Talk pages are built in: it’s just the topic thread. Other projects could make their own wikis at their own URLs using their own tags in the same way. Pages relevant to multiple software packages would appear on multiple wikis automatically!</gush>

  • Someone could build a separate standalone website using some appropriate technology.

  • We could use a GitHub wiki somewhere. I think this is not ideal though, since it’s less of a software-development-centric topic, and more of a scientific one.

  • We could somehow leverage the tags of this forum. This could be in conjunction with a wiki.image.sc site, or not. It would be nice if tags supported descriptions though—otherwise we’d have to document what all the tags mean somewhere else, which would be cumbersome to maintain.

This is awesome. But not open source. So no chance we could reproduce everything there online for the benefit of the community. I fear we will need to build something new with an open license.

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Something like this exists at biii.eu, though it’s not so much a glossary as it is a searchable listing of software / algorithms / methods.

In its own words :

Many tools for Bio Image Analysis are already available but information about these tools is non-uniform and often focuses on technicalities about the methods implemented rather than the problems the tools can actually solve. Since bio image analysts focus on applied problems, this information is often inadequate. To overcome this issue, the platform BISE developed by the Network of European Bio-image Analyst NEUBIAS try to match the problem with the relevant tools.

Edit:
this forum has an entry on biii.eu thanks to @imagejan :slight_smile:

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Well, it is already freely available online…

Only 0-9 and A-G, not H-Z. And only the first edition. And the content is not community editable.

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Oh, yes you are right!

Hi @oburri,
It might be worth having a look at the EDAM-BIOIMAGING ontology directly at https://bioportal.bioontology.org/ontologies/EDAM-BIOIMAGING/
This has been developed partly during the Taggathons at the NEUBIAS meetings over the past few years and is the ontology included on the biii.eu site.

Some entries have definitions (not all) and there are links to the various types of synonyms.
There’s a poster about it here https://f1000research.com/posters/8-158
Note that anyone can contribute, see https://github.com/edamontology/edam-bioimaging#contributing - it’d be great to have the whole community helping to improve it!

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Hi all and thanks for the awesome contributions

Thanks for the link! I admit I sincerely do not know what to think of these entries. I like the fact we can view them from https://biii.eu but it seems they serve the purpose of tagging software rather than offer definitions of operations. Most entries related to something simple, like ‘roi-measure’ link to plugins with a description like ‘roi measurement plugin for ICY’ and nothing liked to a description of what is meant by roi measurements. So I have a hard time seeing how people looking to learn about image analysis terminology can locate information there.

That sounds awesome! As well as the ideas for integrations and the inclusion of the imagej.net pages as Discourse topics! I for one would be much more willing to edit Discourse topics and use them to discuss issues/improvements through here when there isn’t a GitHub Issue.

For the topic of a glossary I seem to agree. We notice that a hard first step for people getting into image analysis is figuring out the vocabulary peope in the field are using. And for the people in the field, it can be difficult being consistent due to the fact that different disciplines and softwares use different terms (Regions of Interest, Annotations, Regions, Area of Interest, Zone of Interest, for example).

I obviously have no solution to this but I greatly appreciate the current discussion with all your great minds and hope more people input their opinions, thoughts and ideas!

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Yes, at the moment, as I understand it, it’s mostly been a vehicle for allowing consistent tagging of software, rather than having a descriptive glossary. However, there is the capacity to include the definitions and it seems to me that it might be better to have these things combined in the broadest way possible, so that the community can agree on the definitions democratically and then they are applied everywhere.

Perhaps, as @ctrueden suggests, a wiki is the best interface for newcomers - which could presumably pull the info from the edam-bioimaging resource? Then the problem shifts to populating these definitions, which could be something similar to the NEUBIAS taggathons (CC @PerrineGilloteaux) or individuals filling them in their spare time.

Since reinventing the wheel is one of the major problems in a lot of image analysis, I’d be keen to try to integrate these resources as much as possible!

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