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Bioimage Analysis Workshop, April, 30–May, 1, 2012, Barcelona, Spain

Bioimage analysis software: is there a future beyond ImageJ?

The workshop brought together developers and users of imaging software for the analysis of biomedical images. Its purpose was to review the state of the art and to establish requirements for future developments. The focus was on JAVA-based open-source solutions---in particular, ImageJ---and other open architectures that facilitate the development of plugins and community-driven projects.

Proceedings

Download the complete booklet [16.1 Mb]

Abstracts
Abstracts of Invited Speakers
Ignacio Arganda-CarrerasImage Registration and Segmentation Paradigms in Fiji
Kevin EliceiriOpen Source BioImage Informatics: Tools for Interoperability
Pavi KankaanpääBioImageXD Image Processing, Analysis and Visualization Platform
Michael LieblingPrototyping Complex Microscopy Imaging Pipelines
Erik MeijeringRobust Cell Segmentation: Half a Century Between Hope and Reality
Jean-Christophe Olivo-MarinIcy–An Open-Source Community Image Processing Software
Wayne RasbandIntroduction to ImageJ
Curtis RuedenImageJ2–ImageJ for the Next Generation of Biological Image Data
Download the slides of the presentation [63.1 Mb]
Stephan SaalfeldImgLib2–Generic Image Processing in Java
Johannes SchindelinFiji–A ImageJ Distribution for the Bioimaging Community
Carlos Óscar SorzanoHybrid C++/ImageJ Visualization System: An Example in Xmipp
Nico StuurmanMicroManager–An Open Software Platform for Control of Motorized Microscopes and Cameras
Jason SwedlowThe Open Microscopy Environment: Open Image Informatics for the Biological Sciences
Philippe ThévenazTurboReg and Other ImageJ Plugins at the Biomedical Imaging
Pavel TomancakA Biologists Perspective on the Challenges in Biological Image Analysis and how the Fiji Platform Attempts to Meet them
Abstracts of Posters
01Parametric Snakes in Microscopy
02Segmentation of EM Images of Neuronal Structures Using CellProfiler
03KNIP–KNIME Image Processing and Analysis
04ALIDA–Automatic Generation of User Interfaces for Data Analysis Algorithms
05BaudJ–Cell Size Computation During the Cell Cycle
06WIDE–Web Image and Data Environment
07Image Analysis Tools Within an Integrated Development Environment for Ecological Modeling at Various Scales
08SynapCountJ–An ImageJ Plugin to Analyze Synaptical Densities in Neurons
09ImageJ-Driven Intelligent High Content Screening
10A Generic Solution for Tile-Based Histological Image Analysis
11Developing Open Source Image Analysis Software in Plant Sciences
12CytoSurfer–Deal with Large Data Sets Generated by Image Segmentation Using ImageJ
13ImgLib2–Concepts and Features
14Icy: One Year Old But Already Grown-Up!
15Remote Visualization, Collaborative Annotation, and Automated Analysis of High-Resolution Bioimages Through Internet
16Extending Imaris Using Java and Launching Fiji Plugins from Within Imaris
17ImageJ Tools for STED Performance Analysis
18A KNIME-Based Workflow for the Distinction of S-Phase Stages in Cells Immunolabeled for PCNA Detection
19Open-Source Software for Single-Molecule Localization Microscopy
20Endrov–An Open Source Framework for Image Processing and Analysis
21Visualization Tool for the Examination of 3D Tracking Results
22Multiview 3D Image Tiling for OPT and SPIM Data
23Applications of Novel Cellular Diagnostics
24PureDenoise–An ImageJ Plugin for Denoising Multidimensional Fluorescence Microscopy Images
25Digital Phantoms as a Tool for Benchmarking and Testing in Cell Imaging
26Graph-Cut Library for Biomedical Image Analysis
27Creating Faster, more Expressive ImageJ Scripts and Plugins with Scala
28ITK Wrapper for Fiji
29FUCCIJ–A Novel Image-Analysis Tool to Construct Cell Lineage Trees from FUCCI Cell-Cycle
30TANGO–A Customizable Tool for High Throughput for Images Analysis of Nuclear Signals
31From Acapella to ImageJ
32Web-Based Collaborative Neuronal Reconstruction with CATMAID
33Improving Acquisition Skills Using Continuous Image Quality Assessment
34CUDA-Based Massively Parallel Implementation of Gray-Scale Mathematical Morphology Operations in Java
35CellFileAnalyzer–Automatic Plant Cell File Length Estimator
36Massive Stitcher–Integrating Plugins for New Tasks

Bioimage Analysis Workshop
The program will feature a series of invited talks by software developers and researchers who have significantly contributed to the field. In addition to the presentations, there will be special slots for posters and demos as well as roundtable discussions for drafting a roadmap for future resource developments in the context of Euro Bioimaging. The workshop includes the following topics:

  • Description of novel open-source image-analysis software
  • Solutions for the analysis of biological and biomedical images
  • Issues in parallel implementations, multidimensional data, scripting, large data sets, distributed computating
  • Standardization mechanisms and accreditation of software
  • Benchmarking and testing
  • Web-based resources

Invited Speakers

  • Ignacio Arganda-Carreras, Seung Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
  • Kevin Eliceiri, LOCI, University of Wisconsin, Madison, WI, USA
  • Pasi Kankaanpää, Turku Centre for Biotechnology, University of Turku, Turku, Finland
  • Michael Liebling, System Bioimaging Lab, University of California, Santa Barbara, CA, USA
  • Jean-Christophe Olivo-Marin, Quantitative Image Analysis Group, Institut Pasteur, Paris, France
  • Erik Meijering, Biomedical Imaging Group Rotterdam, Erasmus MC - University Medical Center, Rotterdam, Netherlands
  • Wayne Rasband, Research Services Branch, National Institutes of Health, Bethesda, MD, USA
  • Curtis Rueden, LOCI, University of Wisconsin, Madison, WI, USA
  • Stephan Saafeld, Tomancak Lab, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
  • Carlos Óscar Sorzano, Biocomputing unit, Universidad Autónoma de Madrid, Madrid, Spain
  • Johannes Schindelin, LOCI, University of Wisconsin, Madison, WI, USA
  • Nico Stuurman, Vale Lab, University of California, San Francisco, CA, USA
  • Jason Swedlow, Swedlow Lab, University of Dundee, Dundee, UK
  • Philippe Thévenaz, Biomedical Imaging Group, École polytechnique fédérale de Lausanne, Switzerland
  • Pavel Tomancak, Tomancak Lab, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany

Program

Monday, April 30
8:30 Registration
installation of posters
9:15 Opening (Michael Unser)
9:20 Wayne RasbandIntroduction to ImageJ
10:00 Pavel TomancakA Biologists Perspective on the Challenges in Biological Image Analysis and how the Fiji Platform Attempts to Meet them
10:25 Jason SwedlowThe Open Microscopy Environment: Open Image Informatics for the Biological Sciences
10:50 Coffee
11:20 Johannes SchindelinFiji–A ImageJ Distribution for the Bioimaging Community
11:45 Jean-Christophe Olivo-MarinIcy–An Open-Source Community Image Processing Software
12:10 Kevin EliceiriOpen Source BioImage Informatics: Tools for Interoperability
12:35 Curtis RuedenImageJ2–ImageJ for the Next Generation of Biological Image Data
13:00 Lunch
14:00 Poster / Demo
14:45 Michael LieblingPrototyping Complex Microscopy Imaging Pipelines
15:10 Nico StuurmanMicroManager–An Open Software Platform for Control of Motorized Microscopes and Cameras
15:35 Erik MeijeringRobust Cell Segmentation: Half a Century Between Hope and Reality
16:00 Coffee
16:30 Philippe ThévenazTurboReg and Other ImageJ Plugins at the Biomedical Imaging
16:55 Ignacio Arganda-CarrerasImage Registration and Segmentation Paradigms in Fiji
17:20 Stephan SaalfeldImgLib2–Generic Image Processing in Java
17:45 Poster / Demo
18:30 Closing of the doors
Tuesday, May 1
8:30 Poster / Demo
9:15 Opening (Michael Unser)
9:20 Pavi KankaanpääBioImageXD Image Processing, Analysis and Visualization Platform
10:00 Carlos Óscar SorzanoHybrid C++/ImageJ Visualization System: An Example in Xmipp
10:25 Organisation of the discussion
10:50 Coffee
11:20 Small group discussions
13:00 Lunch
14:00 Poster / Demo
14:45 Small group discussions
16:00 Coffee
16:30 Round-table
Synthesis
Conclusion
18:30 Closing of the doors

 

Satelitte workshops of ISBI 2012
This workshop is a satellite event of the IEEE International Symposium on Biomedical Imaging (ISBI'2012) which will take place in Centre Convencions International Barcelona CCIB at Barcelona. It is organized 2 days before the ISBI conference. Another workshop focused on Medical Image Analysis will run in parallel.

Organizers
  • Michael Unser, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland
  • Arrate Muñoz-Barrutia, Center for Applied Medical Research, Pamplona, Spain
  • Andreas Jahnen, CRP Henri Tudor, Luxembourg
  • Daniel Sage, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland

© 2012 Biomedical Imaging Group, EPFL • webmaster.big@epfl.ch •  10.07.2012