Shantanu Singh

I completed my Ph.D. in 2011 and am now at the Broad Institute of MIT and Harvard.

shsingh at broad dot mit dot edu / linkedin profile


I am a Ph.D. candidate in the Department of Computer Science and Engineering at The Ohio State University. As part of my dissertation research, I am developing a computational framework for analyzing cells in 3D images of tissue microenvironments and using it to investigate nuclear phenotypes in the tumor microenvironment in breast cancer. During my graduate studies, I interned at GE Global Research and Lawrence Livermore National Laboratory. Prior to joining OSU, I worked as research engineer at Daimler Research.

Quantitative Phenotyping in the Tumor Microenvironment


The focus of my dissertation research is the design of a computational framework to conduct large-scale quantitative phenotyping of cell nuclei from confocal and multi-photon fluorescence microscopy images. The framework is driven by an image analysis workflow to segment nuclei in thick tissue sections, and a mathematical representation of nuclei from which statistical models of morphology are built. The system is supported by visualization tools to explore the models and a system to track all experimental meta-data in the study. This framework provides a structured approach of analyzing and indexing morphologies of cellular level structures on a large scale in 3D within the tissue environment. The framework will enable the study of phenotypical variations at the cellular level, on a large scale, across genetic variations relevant to cancer, and within the spatial context of the tissue architecture.

Segmented and annotated reconstruction of mammary tissue imaged using a Zeiss 510 Meta confocal microscope. Cell nuclei were stained were using DAPI. The image was segmented using ITK filters and the cell type annotations were manually curated.


Journal Conference Workshop Abstract TechnicalReport 

Thesis Related

Singh S, Janoos F, Pecot T, Caserta E, Rittscher J, Leone G, Huang K, Machiraju R. Non-parametric Population Analysis of Cellular Phenotypes. 14th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Toronto, Canada, Sep 2011. [NEW] 

Singh S, Janoos F, Pecot T, Caserta E, Leone G, Rittscher J, Machiraju R. Identifying Nuclear Phenotypes using Semi-supervised Metric Learning, 22nd International Conference on Information Processing in Medical Imaging (IPMI), Irsee, Germany, Jul 2011. [NEW] [url]

Singh S, Raman S, Caserta E, Leone G, Ostrowski M, Rittscher J, Machiraju R. Analysis of Spatial Variation of Nuclear Morphology in Tissue Microenvironments, 7th IEEE Intl. Symposium on Biomedical Imaging (ISBI), Rotterdam, Netherlands, May 2010. [url]

Singh S, Mosaliganti K, Machiraju R. Microstructure preserving synthesis of biomedical images, 5th IEEE Intl. Symposium on Biomedical Imaging (ISBI), Paris, France, May 2008. [url]

Singh S, Raman S, Rittscher J, Machiraju R.  Segmentation Evaluation for Fluorescence Microscopy Images of Biological Objects, 4th Intl. Workshop on Microscopic Image Analysis with Applications in Biology (MIAAB), Bethesda, MD, Sep 2009.

Singh S, Machiraju R, Pecot T, Leone G. Large Scale Phenotyping in Tissue Microenvironments, Visualizing Biological Data (VizBi 2011), Cambridge, MA, Mar 2011.

Singh S, Pecot T, Caserta E, Ostrowski M, Leone G, Huang K, Rittscher J, Machiraju R. Quantitative Phenotyping of Nuclei in the Tumor Microenvironment, Bioimage Informatics, Pittsburgh, PA, Sep 2010.

Singh S, Cooper L, Mosaliganti K, Wallace J, Merchant A, Zhang J, Leone G, Ostrowski M, Machiraju R, Huang K. A Systems Biology Approach to Model Breast Tumor Microenvironment, Bioimage Informatics, Ashburn, VA‎, Apr 2009.


C Pecot T, Singh S, Caserta E, Huang K, Machiraju R, Leone G. Non-parametric Cell Nuclei Segmentation based on a tracking over depth from 3D fluorescence confocal images, IEEE Intl. Symposium on Biomedical Imaging (ISBI), Barcelona, Spain, May 2012. [NEW]

W Mosaliganti K, Singh S, Naidu S, Rittscher J, Bhotika R, Machiraju R, Huang K, Leone G. Estimating Intensity Bias Fields in Confocal Images Showing Salient Cellular Arrangements, 3rd Intl. Workshop on Microscopic Image Analysis with Applications in Biology (MIAAB), New York, NY, Sep 2008.

A Bhattacharya A, Srinivasan R O, Singh S, Huang K, Machiraju R.  PHENOLIMS - Connecting Endothelial Phenotypes with Wound Outcomes, 2nd Annual CCTS Scientific Meeting, Columbus, OH, May 2011.

A Srinivasan R O, Bhattacharya A, Singh S, Huang K, Machiraju R.  Quantitative Image Analysis for the Wound Microenvironment}, 2nd Annual CCTS Scientific Meeting, Columbus, OH, May 2011.


J Janoos F, Machiraju R, Singh SMorocz I A. Spatio–Temporal Models of Mental Processes from fMRI, Neuroimage, Jun 2011

C Janoos F, Singh S, Machiraju R, Morocz I A. State–Space Models of Mental Processes from fMRI, 22nd International Conference on Information Processing in Medical Imaging (IPMI), Irsee, Germany, Jul 2011. 

Video Surveillance

C Janoos F, Singh S, Irfanoglu O, Machiraju R, Parent R. Activity Analysis Using Spatio-Temporal Trajectory Volumes in Surveillance Applications, IEEE Symposium on Visual Analytics Science and Technology (VAST), Sacramento, CA, Oct 2007.

Singh  S, Machiraju R, Parent P. Visual Analysis of Trajectory Clusters for Video Surveillance, OSU-CISRC-2/07-TR11, Feb 2007.


Singh S. Anomaly detection using negative selection based on the r-contiguous matching rule, 1st Intl. Conference on Artifical Immune Systems (ICARIS), Canterbury, UK, Sep 2002.