Webtool: Taggathon


During 3 days, developers and analysts will gather in a room to develop a new community Webtool: a web platform that integrates all documentation, knowledge related to Open and Commercial BioImage Analysis Softwares and interrelates them in a way which will be comprehensive and accessible to the community.

The participants will concentrate on tagging pages, back linking literatures and adding documentation to each page.

The original web-platform is being developed and prepared (see below).

See the motivations and details for this webtool here.


Seats are very limited due (only!) to the size of the room,

participants ("Taggers") are therefore being invited by Euro-BioImaging to take part in the Taggathon.

Ideally, most of Open Software packages will be represented by one developer, e.g. ImageJ, Fiji, ICY, OMERO (OME), KNIME, CellProfiler, BioImageXD, etc...

Additionally, about 10 analysts from Imaging Facilities will participate to the event. They will help bridging developers and users and their broad experience of the bioimage analysis tools will be a precious input.

The list of participants is not closed yet, if you are interested in participating to the event, please express your interest to eubias2013(at)gmail(dot)com

Under discussion is the possibility to broadcast/Tweet the event.


The Taggathon will happen on days 9, 10 and 11th of October in a room of the Barcelona Science Park.

Participants will be expected to attend the Community meeting in order to collect and centralize the recommendations of the community for the construction of the Webtool, which will be discussed on day 2 of the meeting.

The event

    Preparation for the Taggathon

The web-tool platform should be designed before the Taggathon and ready to receive tags during the event. Its functionality could be improved during the Taggathon. There are several aspects in this preparation.

  • Setup a server and install the web-tool (the most likely candidate is mediawiki).

    • Capability of redundant tag is preferable. For example, if many people tag a page with “registration”, the count of this tagging activity would reflect the popularity and consensus.  This could either be shown as a tag cloud or as the actual count.

    • OBIA website could be added with the webtool? Under discussion with Daniel Sage.

    • The web-tool should support access log statistics.

    • Infinite number of tags should be allowed to be added to a page.

  • A person who administrates the webtool.

    • for this we need a volunteer.

  • Ask for a list of functions from developers of each package and create a page for each function. This probably could be done automatically

    • some functions such as “open file” could be useless, but does not harm the tagging activity. We could simply ignore them.

    During the Taggathon

Each participant chooses one software package to work on and to have some feeling of responsibility. Though each participant is then assigned to that package, one could also tag other package functions and it is largely welcome.

Tags can be freely created by each participant.

One could also test various packages with similar functions and add comments on differences, merits and demerits in the function specific page. Such description may cause some conflict between the commenter and the developer, but this should be resolved peacefully among them by discussion.

If possible, taggers will add back links to related pages (e.g. articles that used the function or reference to a scientific article on the underlying algorithm).

Those who attended the Taggathon will have right to edit the webtool after the Taggathon.

The Taggathon 2013 is thought as a novel, proof-of-concept initiative to improve BioImage Software accessibility and is expected to grow further and include more references to other software packages, libraries, etc... in the future.

Please send your comments to eubias2013(at)gmail(dot)com, with subject 'comments about taggathon 2013',
and/or come to the Community Meeting to provide your input before the Taggathon.

    Preview / Mock-ups

The group of Daniel Sage at EPFL (e.g. Ricard Delgado, Virginie Uhlmann) is working on a first version of the online Tool which should be used during the Taggathon, it is being implemented in the beta version of OBIA

Check the current version of the Website: here

Here are some mock-ups / snapshots of how it could look like: