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3-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 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 3-Dimensional Tissue Imaging 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 3-Dimensional Tissue Imaging core are:

  • 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.
  • 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.
  • Integration with the other O’Brien center cores – The 3-Dimensional Tissue Imaging 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 3-Dimensional Tissue Imaging core with renal investigators. The capabilities and services of the 3-Dimensional Tissue Imaging core is promoted through the Enrichment Program, via the O’Brien Center website and the semi-annual workshops.

View core publications

Core Director

5040-Ashkar (El-Achkar), Tarek

Tarek M. Ashkar, MD

Terence P. Kahn Professor of Nephrology


Read Bio Tarek M. Ashkar, MD

Large-scale imaging of human nephrectomy tissue section by fluorescence spectral confocal microscopy. A 50 micron section was stained for 8 fluorophore, spectrally imaged and unmixed. Shown are DAPI in gray, AQP1 in magenta, THP in cyan, F-actin in green.

Large-scale imaging of human biopsy section by fluorescence confocal microscopy. A 50 micron section was stained for 4 fluorophores and imaged. Shown are DAPI in gray, F-actin in green, Myeloperoxidase in red, CD45R in blue.

3D Rendering of human nephrectomy tissue. Immuno-fluorescently stained nephrectomy image volume from Figure 2 was rendered in 3D with Voxx. Nuclei are renderedin gray, F-actin in purple, aquaporin-1 in red and aquaporin-2 in green