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Modeling with Images in the Life Sciences
Description and aim
Modern imaging and image processing is revolutionizing the scientific investigation in the life sciences. However, much current practice is tailored toward specific workflows and use cases that are neither sharable nor generalized appropriately to manifold and diverse scientific questions. One reason for this shortcoming is lack of a standardized image modeling workflow and vocabulary. The purpose of this workshop was to develop a framework for bio-imaging theory by elaborating on the methods and terminology currently applied. Starting from the image as produced by imaging devices at micro-scale resolution, the workshop focused on the exploration of the range of methodologies developed for modeling based on series of images and on establishing common ground for formulation of theory.
A principal aim of this workshop was bringing together different communities that deal with images in the life sciences, and increase understanding in modeling workflows in BioImaging, with a focus on BioImaging at the micro-scale. Effective BioImaging requires collaboration between several distinct research communities, each having their own perspective and vocabulary. A common framework for workflow and vocabulary is a necessity for the communication between scientists, exchange of data (images) and interpretations of these data. Such a framework will help to distill theory from established practices. The workshop covered a spectrum of topics, ranging from image acquisition and processing to interpretation, visualization and analysis.
Each day of the workshop was dedicated to a particular component of imaging workflows, ranging from image acquisition to visualization and analysis. The morning sessions were comprised of a plenary lecture and a plenary discussion session, whereas the afternoon sessions contained another lecture followed by discussions in smaller groups. These sessions in smaller groups resulted in vivid discussions about the workflows in various subfields of BioImaging, covering Brain Imaging, Cell Imaging, Molecule Imaging and Developmental Biology. The division of the subject provided a good format for discussion and the participants took part in different of these group discussions.
The workshop attracted a highly interdisciplinary group of 56 participants from 22 different institutes in 9 countries. The number of junior researchers among the participants was around 20. As a consequence of their mixed backgrounds, including Computer Science, Biology, Chemistry and Mathematics, many participants were unacquainted with each others’ work and methods, and many new contacts were made. This effectively fulfilled a principle aim of the workshop: bringing together researchers from various communities involved in BioImaging and setting up dialogues. Two poster sessions and software demonstration, specifically aimed at the young researchers, allowed for the participants to present their own work.
To preserve the outcome of the many discussions, a Wiki site was set up and for each discussion session, a moderator made a written report available. These results can now serve as a starting point for defining workflows and a common vocabulary and discussion framework in BioImaging. The general discussions, in plenary sessions, during lunch and coffee breaks taught us that possibilities to annotate all parts in the imaging workflow in an unambiguous manner are very much required. In addition, many new initiatives for collaborations between the participants were started. Examples include: Leiden-Antwerpen, Antwerpen-PSI (Switzerland), Leiden-Amsterdam, Leiden-Groningen, Turku-Leiden, Praag-Leiden.
Organization and Funding
The organization of the workshop by the Lorentz Center staff, in particular Mrs. Pauline Vincenten, Dr. Henriette Jensius and Dr. Mieke Schutte, was very smooth and gave the participants full freedom to enjoy the workshop in a relaxed and inspiring environment.
The organizers would like to express their gratitude towards the Lorentz Center, and gratefully acknowledge financial support of the KNAW and the Cyttron II project.
Joost Batenburg (CWI, University Antwerp)
Fons Verbeek (Leiden University)