New Bioimaging Informatics effort at MIC
There is a current imbalance between an auto-/semiautomated image acquisition processes and de facto manual image analysis. MIC, through a concerted effort with the UiB and BCCS, bioinformatics environment, aims to establish easy access and user support to state-of-the-art bioimaging software tools for (i) storage, (ii) retrieval, (iii) auto-mated analysis and (iv) visualization of the rapidly increasing collection of biomedical image recordings and modalities in modern laboratories.
MIC aims to establish a integrated sub unit that will do R&D on imaging analysis method and turn findings and other available freeware into services. Images and accompanying meta-data will be stored centrally (securely with backup) so that they can easily be retrieved. Access will be provided online for the owner of the data. Software tools for image analysis and quantification will be implemented/developed and a user friendly interface created to reduce the threshold in practical use. Support will be provided for both the storage/retrieval procedures, and for the development and use of advanced software tools as well as for tailoring both to specific projects.
R&D challenges in particular involves developing software for *Segmentation of cells (surface stained, cytoplasma stained and DIC images) and subcellular components *Automated detection and localization of signals from fluorescence stained biomolecules *Tracking of objects (cells, organelles / vesicles and molecules) in dynamic recordings *Registration (spatial alignment) of images taken at different times or under different experimental conditions for assessment of changes in size, shape or signal intensities, or of objects recorded with different imaging modalities for multispectral analysis and pattern classification *Analysis of functional 3D+time imaging series in small-animal MRI related to perfusion and diffusion *Modelling of cells behaviour and biological processes towards image-based systems biology.
With regard to service connected to storage we aim to prepare systems for storage, transfer, conversion and retrieval of image data (MySQL). With regard to tools for image analysis we aim to tailor and make universally available for users *software from the Open Microscopy Environment (http://openmicroscopy.org ) * software from the CellProfiler Software Project (http://www.cellprofiler.org/) *High Content Microscopy analysis software for analysis of High Throughput Imaging *integrations of the above and other existing software (Imaris, ITK, VTK, MIPAV, Matlab) *create a user-friendly interface for the above software and issue these as freeware *create user documentation.
With regard to support we aim to provide support on all levels ranging from *introductory courses *providing necessary introductory support *setting up/tailoring software for specific analysis series *carrying full series of especially demanding analysis. Moreover, advanced courses in biomedical image processing, analysis and visualization will be connected to the new Interdisciplinary Research Training Program in Medical Imaging headed by Prof. Olav Haraldseth (NTNU).
Funds have been applied for with the NRC under the INFRASTRUKTUR call, but we will aim to establish as much as possible of the above regardless of receiving funding or not.
For further information please consult the attached project description (below).