About

Each component and workflow pages are tagged manually with biological and/or image processing term, to develop mutual and organic links between biological and image processing regimes. For more about the aim of this site, please read About and EuBIAS Manifesto.

We started constructing Biii on Oct. 11, 2013 during the first taggathon in Barcelona. We made major upgrades and added ca 140 pages of workflows in the second taggathon in Paris in Dec. 2014.

What BIII can do for you, what you can do for BIII

Existing software packages afford a rich range of tools for processing and analysis of microscope images. They are constantly evolving and the number of functions is steadily growing. With so many choices offered to the users, the problem to choose the best tool to answer a specific question is not trivial and is sometimes extremely complex. There is a gap between the rich availability of tools and the users. A simple list of links to software packages does not help much.

We need to have a bridge. Biii (BioImage Information Index) is this bridge, allowing you to search for a tool you need for your bioimage analysis. At the same time you could contribute to this site by adding functions and packages, tagging functions, commenting and evaluating tools.

Biii will continue to evolve, enhancing its usability and its contents.

For more details, please see "The webtool" section in the EuBIAS Manifesto.

Taggers

The following "taggers" attended the first taggathon in EuBIAS, Oct 9 - 11, 2013 and created this site:

  • Jason Swedlow, Univ. Dundee & EuroBioimaging WP11
  • Kota Miura, EMBL Heidelberg
  • Julien Colombelli, IRB Barcelona
  • Sébastien Tosi, IRB Barcelona
  • Perrine Paul-Gilloteaux, Curie, Paris
  • Christian Tischer, EMBL Heidelberg
  • Christoph, Moehl, DZNE Bonn
  • Thomas Pengo, CRG Barcelona
  • Simon F Nørrelykke, ETH Zurich
  • Carlos Ortiz de Solórzano Aurusa, CIMA, Pamplona
  • Petr Walczysko, Univ. Dundee (OME)
  • Ricard Delgado Gonzalo, BIG - EPFL
  • Thomas Walter, Mines Paris
  • Johannes Schindelin, LOCI, Univ. Madison (Fiji / ImageJ)
  • Fabrice de Chaumont, Pasteur, Paris (ICY)
  • Martin Horn, Univ. Konstanz (KNIME)
  • Lee Kamentsky, Broad Institute, Boston (CellProfiler)
  • Christoph Sommer, IMBA Vienna (CellCognition)
  • Ullrich Kloethe, U. Heidelberg (VIGRA)
  • Nicolas Rey-Villamizar, Houston (Farsight)
  • Laszlo Marak, ESIEE (PINK)
  • Stuart Berg, Janelia Farm, HHMI (Ilastik)
  • Luis Pedro Coelho, EMBL Heidelberg (Mahotas)
  • Joe Barry, EMBL Heidelberg (EBImage)
  • Peter Majer, Bitplane (Imaris)
  • Ronald Ligteringen, Delft University of Technology (DIPimage)
  • Fabrice Cordelières, Bordeaux Imaging Center
  • Ofra Golani, Weizmann, Rehovot
  • Chong Zhang, CellNetworks, Univ. Heidelberg
  • Nikolay Kladt, CECAD, Koeln
  • Graeme Ball, Univ. Dundee

The following "taggers" attended the second EuBIAS taggathon, Dec 8 - 9, 2014, and worked on upgrading the web functinality and adding 140 workflows:

  • Perrine Paul-Gilloteaux, Institut Curie, Paris
  • Kota Miura, EMBL Heidelberg / NINS Tokyo
  • Julien Colombelli, IRB Barcelona
  • Sébastien Tosi, IRB Barcelona
  • Christoph, Moehl, DZNE Bonn
  • Thomas Pengo, Univ. Minnesota
  • Simon F Nørrelykke, ETH Zurich
  • Fabrice Cordelières, Bordeaux Imaging Center
  • Chong Zhang, CellNetworks, Univ. Heidelberg
  • Nikolay Kladt, CECAD, Koeln
  • Graeme Ball, Univ. Dundee
  • Peter Bankhead, QUB UK, Belfast
  • Olivier Burri, EPFL, Lausanne
  • Torsten Stöter, LIN Magdeburg
  • Laurent Gelman, FMI Basel
  • Marie-Laure Boizeau, ex-Itav, Toulouse
  • Nicolas Signolle, Institut Curie, Paris
  • Volker Bäcker, MRI, Montpellier

Acknowledgements

This site, biii.info, is supported by EuroBioimaging Working Package 11 "Data Storage and Analysis". The second taggathon was supported by France BioImaging.

Ricard Delgado Gonzalo (BIC-EPFL), together with Virginie Uhlmann and Daniel Sage (BIC - EPFL) contributed largely in setting up the tagging platform initially used during the taggathon. This prototype site could be found here.

During Oct 2013 - Nov. 2014, Biii.info existed in ImageJ.dev server. We thank Johannes Schindelin and Curtis Rueden for their kind offer and their generous supports! From Dec. 2014, the site is running in EMBL web server. We thank Agustin Villalba Casas and Matthias Helmling (IT service, EMBL Heidelberg) for their help in migrating the site.