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Molecular Imaging Core

The Molecular Imaging Core of the Indiana O'Brien Center for Advanced Microscopic Analysis provides assistance in the interrogation and analysis of experimental animal and human-derived kidney tissue.

Research Services

Co-Detection by Indexing (CODEX)

This technology enables multiplexed immunofluorescent imaging of more than 40 markers in the same tissue section (10 μm thick OCT or FFPE) using DNA-conjugated antibodies using the CODEX PhenoCycler (AKOYA Biosciences). Tissue cytometry (segmentation, exploration, quantification) is subsequently then conducted using our customized VTEA software.

Large-scale 3D imaging and Tissue Cytometry (3DTC)

3DTC generates high-resolution confocal fluorescence image volumes of 50-micron thickness from entire kidney tissue sections. When required, spectral unmixing of 16 channel fluorescence images is conducted to generate 3D images of up to 8 fluorescent probes. Concomitantly, multiphoton microscopy is conducted to collect second-harmonic generation (SHG) images of collagen deposition (fibrosis),which is registered as a 9th channel. The resulting image volume will undergo cytometry analysis with our customized VTEA software. VTEA is specifically designed to support interactive exploration of the image volume and conduct quantitative analyses of the abundance, distribution, and characteristics of each cell type, as defined using supervised or unsupervised classification approaches.

Spatial transcriptomics (ST) including multiplexed in situ sequencing

The ST technologies utilizes the 10x Visium, Visium HD, or Xenium platform. These technologies map transcriptomic signatures of kidney cell types and states over a histologic image. A 7-10 μm section of an OCT or FFPE core is placed inside a fiducial capture zone on a slide.

The core provides analytic support to ensure the outputs of molecular imaging are interpretable and integrated within and across technologies, and data outputs are consistent with best practices and are harmonized with cell-type and state definitions used across the renal community. The technologies can be offered individually to facilitate spatial anchoring of proteomic and transcriptomic signals, or offered together, sometimes on the same tissue specimen. An integrated output can be accomplished by direct co-registration on consecutive sections or alignment in the analytical space.

The technologies offered through the Molecular Imaging Core will allow investigators to define, localize and quantify cell populations, cell-cell interactions within 3D neighborhoods, morphological changes and injury regions, the expression of up to 18,000 genes mapped over histopathology, and deep immune and injury phenotypes anchored spatially.


  • Develop a service that provides high quality, optimized imaging of human and animal kidney tissue. Through our involvement in the Kidney Precision Medicine Project (KPMP) and Human Biomolecular atlas project (HuBMAP) consortia, the proposed technologies underwent rigorous external review using a peer review process. Such experience has resulted in a robust analytical pipeline with defined metadata and quality control (QC) metrics for each technology. We will similarly emphasize QC in the Indiana O’Brien Center to ensure highly reproducible data is generated for the renal community.

  • Develop a service that supports remote digital analysis. Services include management of users’ image and sequencing 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.

  • Integrate across O’Brien Center technologies. The Molecular 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 Molecular Imaging core with renal investigators.

Core Directors

5040-Ashkar (El-Achkar), Tarek

Tarek M. Ashkar (El-Achkar), MD

Terence P. Kahn Professor of Nephrology

Read Bio Tarek M. Ashkar (El-Achkar), MD

5161-Eadon, Michael

Michael T. Eadon, MD

Associate Professor of Medicine

Read Bio Michael T. Eadon, MD