Similar to a general assembly of the BioImaging Community, this 2-days meeting follows the Satellite Meeting of ISBI 2012, which has lead to the creation of OBIA.

The idea was seeded at the last EuroBI-WP11 meeting at ELMI 2013 in Arcachon, where a clear need was identified to gather all players of the BioImage Community and debate which directions to take, and what bridges to build between developers, analysts and users, in order to ensure open and optimal technology transfer 'from algorithms to bedside'.

Day 1                        Monday 7th of October 2013

Arrival of Delegates

8h - 11h

  • Coffee from 10h.

Session 1: BioImage Community: Status Quo.

11h- 12h15

Why this meeting? You BIAS, the concept: Open bioImaging community - Developers, Analysts, Users -

    • By Kota Miura, 15min.

OBIA & Euro-BioImaging WP11: Status Quo

    • By Jason Swedlow, 15min.

Self-introduction by analysts

    • Moderator: Kota Miura
    • 20 min.
    • Many analysts do not know each other. We give some volunteers an opportunity to be on stage, introduce themselves and briefly describe their background, work and favorite image analysis platforms.

Panel discussion: What to expect from this meeting?

    • Moderator: Kota Miura
    • 25 min.
    • Six selected people will stand on the stage and tell the other people what they expect from the open-community meeting. The audience will be further asked for opinions and suggestions.


12h15 - 13h00  Lunch at the cafeteria

13h15 - 14h00  Coffee at the Auditorium

Session 2: Open Software Showcase - Part 1 -

    • Showcase and strategies/directions of various open software packages or libraries.
    • Invited speaker presentations, 20 min each including questions.

14h00: ImageJ / Fiji

    • "Fiji: A community-driven platform for open science", by Johannes Schindelin

14h20: ImgLib /ImageJ 2

    • "ImgLib2: Generic image representation and processing", by Tobias Pietzsch

14h40: CellProfiler

    • "Image analysis using CellProfiler", by Lee Kamentsky

15h00: CellCognition

    • "CellCognition: Time-resolved phenotype annotation in high-throughput live cell imaging", by Christoph Sommer

15h20: Ilastik

    • "Ilastik: Easy image analysis for non-experts", by Stuart Berg

15h40: VIGRA

    • "VIGRA: A flexible workhorse library for fundamental image analysis algorithms", by by Ullrich Köthe

Coffee break

16h00 - 16h20

16h20: KNIME

    • "Image processing and analysis with KNIME", by Martin Horn

16:40: CreaTools

    • "CreaTools: A development framework for medical image processing software", by Claire Mouton

Session 3: Commercial software bridging open software - Part 1 -

17h00: Bitplane (Imaris) 

    • "Imaris Open", by Luciano Lucas

17h30: Strand Life Sciences (Avadis iManage)

    • "Open Access - An efficient way to connect commercial and open source software", by Anup Kulkarni

Coffee break

18h00 - 18h20

Session 4: Applications/ New Developments from Scientific Computing - Part 1 -

18h20: Pavel Tomancak (MPI-CBG, Dresden)

    • "Using Fiji for processing light sheet microscopy data"

18h50: Luis M Escudero (IBiS, Sevilla):

    • "Application of network theory to the analysis of tissue organization in development and disease"

19h10: Albina Asadulina (MPI-DB, Tuebingen):

    • "Gene expression atlases"

19h30: Thomas Pengo (CRG, Barcelona):

    • "Quantitative measurements in super-resolution microscopy using PALMsiever"

Informal conference Dinner

21h00 - 23h00, more information to come soon

Day 2                        Tuesday 8th of October 2013

Session 5: Commercial Software bridging Open Software - Part 2 -

9h00: Leica Microsystems

    • "Leica tools for microscope control integration", by Francisco Porto

9h30: Carl Zeiss

    • "Open Application Development (OAD) in Zen Blue", by Markus Neumann

Session 6: Applications /New Developments from Scientific Computing - Part 2 -

10h00: Jason Swedlow (Univ. of Dundee):

    • "Illuminating Cell Division with Multi-Dimensional Imaging and Image Analysis"

10h30: Ofra Golani (Weizman, Rehovot):

    • "BioImg Storage Server"

10h50: Mathieu Leclaire (ISCPIF, Paris):

    • "OpenMOLE: access to parallelisation with zero effort"

Coffee break

11h10 - 11h40

Session 7: Open Software Showcase - Part 2 -

11h40: OME (Bio-Formats & OMERO)

    • "OME: Open Image Informatics for the Biological Sciences", by Jason Swedlow

12h00: ICY

    • "Image analysis with Icy", by Jean-Christophe Olivo-Marin

12h20: DIPImage

    • "DIPimage - a MATLAB toolbox for scientific image processing and analysis", by Bernd Rieger

12h40: ITK / Farsight

    • By Nicolas Rey-Villamizar, univ. of Houston

13h00: Pink

    • "The Pink Image Processing Library", by Laszlo Marak

13h20: Mahotas

    • "Using Mahotas and the Python Ecosystem to build bioimage informatics applications", by Luis Pedro Coelho

13h40: EBImage

    • "EBImage showcase", by Joe Barry

Lunch and Posters

14h00 - 15h45,  at the Terrace or in the basement Hall, weather-dependent)

Session 8: Open Community Panel Discussions

Selected participants go up on the stage and discuss about a specific topic and interacts with the audience. The topics revolve around the need for a true community of users, analysts and developers, the expectations of each of us and how to work together in the most efficient way to disseminate and conduct cutting-edge bioImage analysis.

15h45: Topic 1- Accessibility to "BioImage Data Analysis"

Many software packages and image processing libraries are available and still increasing in number while biologists in wet labs are often struggling with analyzing images. How could we overcome this problem?

Panel: Users, analysts and developers

  • 1a. First of all, what is great about bio-image analysis?

  • 1b. How was the showcase meeting? Any possible improvements in its design?

  • 1c. What is your opinion about the activities of this symposium (open meeting, course on bioimage analysis, "Taggathon")?

  • 1d. More ideas for improving the accessibility to the bioImage tools?

16h10: Topic 2 - User Requests

We will try to list up the missing ingredients so that the users can take full advantage and get aware of the true potential of image analysis.

Panel: Selected users

  • 2a. From the user side, what do you request to the analysts and developers?

  • 2b. What type of knowledge are lacking for your everyday image analysis?

  • 2c. How could the biologists be motivated to make a greater use of automated image analysis?

  • 2d. How could the interaction between biologists and analysts be enhanced?

16h30: Topic 3 - Improving the environment of developers

What would be the ideal environment for developers? We will discuss on the demands of the developers to the image analysis community.

Panel: Selected developers

  • 3a. Any community effort required?

  • 3b. Being involved in software/library development, what do you need from biologists, analysts and microscopists?

  • 3c. How to efficiently couple algorithm development and neat software engineering (optimization, stability, usability)?

  • 3d. The "interoperability" was a keyword that came up in the meeting in 2012. Have you seen progresses?

16h50: Topic 4 - The community of Analysts

The community of bioimage analysts is somewhat new. We discuss about how to strengthen the network, place the community on the map and also on how to increase communication with developer/engineers of software and libraries. In addition, we will try to find out current shortcomings in the status of software / libraries.

Panel: Selected analysts

  • 4a. How could we foster more interactions among analysts and algorithm developers?

  • 4b. As a profession: The bright side and the dark side of analysts. What has been good and bad working as an image analyst? How do we maintain the community of analysts?

  • 4c. What are the current shortcomings in terms of the modularity of software / libraries?

  • 4d. How could we encourage institutions to open new analyst positions?

17h10: Topic 5 - Funding

We will discuss on the funding of the activity of image analysis community.

Panel: Selected senior scientists and company delegates.

  • 5a. How the image analysis community could be funded?

  • 5b. Is there a future for collaboration between the open scene and companies?

Final Remarks

17h45 - 18h00

Summary of the discussions and perspectives.