Web tool and taggathon

The 2nd taggathon of EuBIAS @ Institut Curie, Paris

 

Image analysts have gathered in Paris and work on biii.info to organize image analysis tools, scripts and libraries, and tag them (the taggathon). This time we have been focusing on workflows, and now provide also some sample data, interleaved by fruitful discussions on our community.
Please register as well in order to tag, rate, upload sample data, create new workflows and components!

Thanks to all our 2015 taggers! We thanks France Bio imaging node Institut Curie for its support and all the taggers’ institutes.

We were happy to host for this 2nd edition of the taggathon:

Ball Graeme (University of Dundee, UK)
Bankhead Peter (Queen’s university, Belfast, UK)
Boizeau Marie-Laure (Inserm, Toulouse)
Burri Olivier (EPF Lausanne, Switzerland)
Colombelli Julien (IRB Barcelona, Spain)
Cordelières Fabrice (University of Bordeaux, France)
Gelman Laurent (FMI, Switzerland)
Kladt Nikolay (University of Koeln, Germany)
Miura Kota (EMBL, Heidelberg, Germany)
Moehl Christoph (DZNE Bohn, Germany)
Norrelykke Simon (ETH Zurich, Switzerland)
Paul-Gilloteaux Perrine (Institut Curie CNRS, Paris, France)
Pengo Thomas (University of Minnesota, USA)
Signolle Nicolas (Institut Curie, Paris, France)
Stöter Torsten (University of Magdeburg, Germany)
Tosi Sébastien (IRB Barcelona, Spain)
Volker Baecker (MRI Montpellier, France)
Zhang Chong (University of Heidelberg, Germany)

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Image analysts will gather in Paris and work on biii.info to organize image analysis tools, scripts and libraries, and tag them (the taggathon). For more details, see the abstract below and also the protocol from last year.

Date & Time

Dec. 8th 11am – Dec. 9th 6:30pm 2014

 

Registration

No registration is required, the event is only opened to invited bioimage analysts taggers.

 

Place

Institut Curie, BDD annexe 1 and 2, , rue Pierre et Marie Curie, 75005 Paris (map)

Food and Beverages

Two lunches, a dinner and 4x coffee breaks will be provided.

Travel and Accommodation

Please organize your travel by yourself! Here are our recommendations:

Taggathon Topics

The main activity:

To increase the “Workflow” contents of Biii.

Other administrative discussions

  1. Improving the structure of Biii for a better usage
  2. Biii maintainance issues, advertisement
  3. Reactivation of EuBIAS mailing lists
  4. EuBIAS 2016 planning

Please read the abstract below for more details.

Schedule (Tentative)

  • day1:
    • 11:00 kickoff, agenda
    • 13:00 lunch
    • 14:00 – 19:30 session 1 (interleaved by two Shout Your Problem* slots)
    • 20:00 dinner (social aspects between analysts are important…)
  • day 2:
    • 10:00 – 13:00 session 2 (interleaved by one Shout your Problem)
    • 13:00 lunch
    • 14:00 – 18:00 session 3 (interleaved by one shout your problem)
    • 18:00 summary of the taggathon & concluding remarks, 30 minutes.

*”Shout Your Problem” is free presentation slot for raising issues to others during taggathon.

 

Organizers

  1. Kota Miura, EMBL Heidelberg, Germany
  2. Perrine Gilloteaux, Institut Curie, Paris
  3. Jean Salamero, Institut Curie, Paris
  4. Sébastien Tosi, IRB Barcelona, Spain
  5. Julien Colombelli, IRB Barcelona, Spain

This taggathon is supported by French Bioimaging.

 

Abstract

Bioimaging requires image analysis. While there are many image processing and analysis tools, it is not a trivial task for researchers to extract numerical information from raw microscopy image data. This is not only due to the technical expertise required, but also due to the difficulty in selecting an appropriate image analysis method to address a specific biological question. Guidelines to choose and combine these tools in a scientific, efficient and quantitative way are largely missing. European BioImage Analsyis Symposium (EuBIAS), an initiative launched in 2013, includes various types of activities to solve this problem by linking biological questions to image analysis solutions (see here).

As a part of EuBIAS, we started up a website biii.info in 2013 to organize the information on image analysis tools, workflows and functions (see the roadmap). The proper choice of the right workflows and algorithm pipelines to tackle a specific problem is largely dependent on technical knowledge and awareness of the tools available. The aim of biii.info is to share this knowledge and guide the end users in this process.

The unique aspect of the biii.info website is that its contributors (we call them “taggers”) manually annotate (we call this activity “tagging”) available workflows and functions.  Tags then allow bioimaging researchers to search for appropriate workflows and functions according to their biological and image processing questions. Tools / workflows / functions will be dynamically linked both internally and externally. We expect that, as the website content  grows, it will become a useful reference for those who got lost while finding and/or building up biological image analysis protocols.

Though contribution to biii.info (tagging) could be performed individually, from the office of each image analysts and image processing engineers via Internet, such voluntary effort tends to diminish. At the same time, the number of available implementations of image processing algorithms is growing each day. To keep the motivation active and not to lag behind the rapid evolution of the image processing scene, we organize periodic “taggathon” where image analysts and image processing engineers sit together to make a social effort to increase the content of biii.info. The intention of this social program is not limited to drive the momentum to enrich the website content. We also expect that taggathons enhance the communication among image analysis specialists and image processing engineers, and strengthen this human network. In addition, taggathons provide a window of time to concentrate on the information collection, organization and discussion on available image analysis workflows and functions. We unfortunately often label this critical task as less priority compared to the specific bioimage analysis problem we are facing in our daily work. In the first taggathon in Barcelona, we refined the concept of the website through extensive discussions, launched the website and started to tag many image analysis functions.

The second taggathon will be held in Institut Curie in Paris, on 8th and 9th of December 2014. We will then focus on increasing the workflow content and also to add biological tags, to widen the bridge between image processing algorithms and biological questions. This taggathon is supported by the French National Research Agency through the “Investments for the Future” program (France-BioImaging, ANR-10-INSB-04)”.