Bioimage informatics for experimental biology

Abstract

Over the past twenty years there have been great advances in light microscopy with the result that multidimensional imaging has driven a revolution in modern biology. The development of new approaches of data acquisition is reported frequently, and yet the significant data management and analysis challenges presented by these new complex datasets remain largely unsolved. As in the well-developed field of genome bioinformatics, central repositories are and will be key resources, but there is a critical need for informatics tools in individual laboratories to help manage, share, visualize, and analyze image data. In this article we present the recent efforts by the bioimage informatics community to tackle these challenges, and discuss our own vision for future development of bioimage informatics solutions.

Figure 1

Architecture of OME and OMERO server and client applications. (A) Architecture of the OME Server, built using Perl for most of the software code and an Apache web server. The main client application for the server is a web browser-based interface. (B) The architecture of the OMERO platform, including OMERO.server and the OMERO clients. OMERO is based on the JBOSS JavaEE framework, but also includes an alternative remoting architecture called ICE (60). For more detail, see (41).

Figure 2

Workflows in WND-CHARM. (A) List of feature types calculated by WND-CHARM. (B) Workflow of feature calculations in WND-CHARM. Note that different feature groups use different sets of processing tools.