Department of Medicine


Three-Dimensional Tissue Imaging Core


Recent developments in optical sectioning microscope systems have provided biomedical researchers with the capability to conduct high-resolution, high-content 3D microscopy at the scale of millimeters, if not centimeters in biological tissues. Image volumes of this size and complexity are enormously rich in potential information. However, microscopy at this scale introduces new sets of challenges with respect to data handling, image visualization and quantitative analysis that limit the ability of most researchers to realize this potential. The overarching goal of the 3-dimensional Tissue Imaging (3DTI) core is to make large-scale, quantitative 3D microscopy accessible and productive for renal researchers, regardless of their institutional infrastructure or their expertise in imaging.

Service of the 3DTI core consists of two components. First, the core is to provide imaging services, which will consist of preparing a sample for fluorescence microscopy, collecting high-resolution image volumes by confocal microscopy, and combining these image volumes into a single hyper-volume. Second, the core will provide access, training and support to investigators in the use of a high-performance image analysis system that can be used by remote investigators in a client-server format. Taking advantage of the advanced computer and networking infrastructure of Indiana University, this system will be designed to provide remote investigators with a powerful, yet easy-to-use tool for interactive exploration and analysis of their image data.

The goals of the 3DTI Core are:
1. Develop a service that provides large-scale, high-resolution 3D microscopy of kidney tissues provided by renal investigators. Services include labeling and preparation of tissues for imaging, 3D confocal microscopy and post-collection assembly of mosaics of 3D volumes into single hypervolumes. Developmental efforts of the core consists of optimizing standard operating procedures and developing alternative approaches for image preparation and collection.

2. Develop a service that supports remote digital analysis of large-scale 3D image volumes via a high-performance image analysis system. Services include management of users’ image data, training and support in the use of volume visualization, image processing, image analysis and data analysis tools, consultation on data interpretation and development of customized strategies of image analysis to support individual projects.

3. Integration with the other O’Brien center cores – The 3DTI core is closely integrated with the Digital Analysis Development Core, which develops and supports the Distributed and Networked Analysis of Volumetric Image Data, (DINAVID) high-performance image analysis system and develops new tools in response to needs identified in interactions of the 3DTI with renal investigators. The capabilities and services of the 3DTI core is promoted through the Enrichment Program, via the Indiana O’Brien Center website and the semi-annual workshops.

Core Director 

Tarek M. Ashkar, MD