Shilpa Dilip Kumar, PhD

Bachelor of Engineering - Visvesvaraya Technological University, Bangalore, India.

Master of Science - Illinois Institute of Technology, Chicago, USA.

Ph. D. - Indian Institute of Science, Bangalore, India.

Post-doctoral fellowship - Institute of Stem Cell Biology and Regenerative Medicine, Bangalore, India.

Post-doctoral fellowship - Columbia University, New York, NY, United States.

I am a biomedical engineer with expertise in applied optics, fluorescence microscopy, and computational image reconstruction. My research interests lie in developing multidimensional image reconstruction methods that improve the spatial, temporal, and quantitative performance of fluorescence microscopy. My doctoral research focused on overcoming the resolution limitations of optical imaging systems through a combination of theoretical modeling and experimental innovation. This included developing point spread function (PSF) simulations, image reconstruction algorithms, and novel optical configurations to enhance image resolution and acquisition efficiency. My work bridges optical engineering and computational microscopy, enabling improved visualization and quantitative analysis of biological systems.

My passion for advanced, state-of-the-art microscopy and expertise in image analysis and reconstruction led me to join the Microscopy and Advanced Bioimaging Core at the Icahn School of Medicine at Mount Sinai as a Senior Scientist, and I was later promoted to Research Assistant Professor. In this role, I collaborated closely with researchers to optimize experimental design, image acquisition, and quantitative image analysis using cutting-edge microscopy platforms and analysis software. My primary responsibility was supporting the facility's multiphoton microscope, where I helped investigators develop efficient imaging workflows and acquire high-quality, high signal-to-noise ratio (SNR) datasets. I also trained researchers on a broad range of imaging systems, including widefield, confocal, and super-resolution STED microscopes, enabling them to effectively utilize these advanced technologies. In addition, I developed and taught image analysis workflows that empowered users to extract robust, quantitative, and biologically meaningful information from their microscopy data, thereby enhancing the rigor and reproducibility of their research.

In my current role as an Assistant Professor (non-tenure track) at the University of Maryland School of Medicine (UMSOM), I support researchers in the effective use of advanced fluorescence microscopy technologies through the Confocal Microscopy Core Facility. My primary focus is on super-resolution imaging, particularly Stimulated Emission Depletion (STED) microscopy, where I collaborate with investigators to develop optimized sample preparation protocols, design imaging strategies, and train users to acquire high-quality, publication- and grant-ready super-resolution datasets. Beyond image acquisition, I provide expertise in quantitative image analysis, guiding researchers in the use of advanced image processing software and AI-based segmentation and machine learning tools to extract robust, reproducible biological information from their data. I am also actively engaged in microscopy education and workforce development, having organized and taught workshops, recurring seminar series, and formal courses on quantitative image analysis for faculty, graduate students, postdoctoral fellows, and research staff. These educational initiatives, originally established at the Icahn School of Medicine at Mount Sinai, have expanded to the University of Maryland School of Medicine and have benefitted researchers across the University of Maryland, Baltimore County (UMBC), and Morgan State University, fostering interdisciplinary collaboration and broadening access to advanced bioimaging technologies.

1. G. J. Krause, P. Kirchner, B. Stiller, K. Morozova, A. Diaz, K. Chen, N. J. Krogan, E A-Pascual, C C. Clement, D L. Swaney, S Dilip Kumar, J Jr Bravo-Cordero, L Santambrogio, A M Cuervo, Molecular determinants of the crosstalk between endosomal micro-autophagy and chaperone-mediated autophagy, Cell Rep., 42(12):113529, 2023.
2. G. M. Riboldi, R. A. Vialle, E. Navarro, E Udine, K P Lopes, A Allan, M Parks, B. Henderson, K Astudillo, C Argyrou, M Zhuang, T Sikder, O Narcis J, S Dilip Kumar, W. Janssen, A Sowa, G P Comi, A Fonzo, J F. Crary, S J Frucht, T Raj, Transcriptome deregulation of peripheral monocytes in GBA-related Parkinson’s disease, Mol Neurodegeneration 17, 52, 2022.
3. A. Mohanty, R. Zunino, V. Soubannier, S. Dilip Kumar, A new functional role of mitochondria-anchored protein ligase in peroxisome morphology in mammalian cells, Journal of Cellular Biochemistry, 122(11):1686-1700, 2021.
4. A. Mukherjee, R. Singh, S. Udyan, S Manmadhan, P Pothula, S. Dilip Kumar, R. Das, B. Rao and A. Gulyani, A Fyn - specific biosensor reveals localized, pulsatile kinase activity and spatially regulated signalling crosstalk, eLife, 9:e50571, 2020.
5. Rao, A. Ketkar, N. Kedia, V. K. Krishnamoorthy, V. Lakshmanan, P. Kumar, A. Mohanty, S. Dilip Kumar, S. Raja, A. Gulyani, C. Chaturvedi, M. Brand, D. Palakodeti, and S. Rampalli, KMT1 family methyltransferases regulate heterochromatin –nuclear periphery tethering via histone and non-histone protein methylation, EMBO Reports, e43260, 2019.
6. Bansal, J. Kulkarni, K. Nadahalli, V. Lakshmanan, S. Krishna, V. Sasidharan, J. Geo, S. Dilip Kumar, R. Pasricha, A. Gulyani, S. Raghavan, D. Palakodeti, Cytoplasmic poly (A) binding protein (PABPC2) critically regulates epidermal maintenance and turnover in planarian Schmidtea mediterranea, Development 144,17, 2017.
7. S. Dilip Kumar, Cubic B-Spline interpolation-based image reconstruction for fluorescence microscopy, AIP Advances, 5, 037103, 2015.
8. S. Dilip Kumar, R. Manjithaya and P. P. Mondal, Multispectral Bayesian Reconstruction Technique for Real-time Two-Color Fluorescence Microscopy, RSC Advances, , 5, 13175, 2015.
9. P. P. Mondal, S. Dilip Kumar and Kavya. M, Efficient generation of Diffraction-Limited Multi-sheet Pattern for Biological Imaging, Optics Letters, 40(4), 609, 2015.
10. A. A. Jabbar, S. Dilip Kumar, C. K. Rasmi, K. Rajan and P. P. Mondal, Real-time Maximum-a-posteriori based 3D Image Reconstruction for Fluorescence Microscopy, AIP Advances, 5, 084801, 2015.
11. S. Dilip Kumar, S. Montalescot and P. P. Mondal, Image reconstruction enables high resolution imaging at large penetration depths in fluorescence microscopy, Appl. Phy. Lett., 103, 173703, 2013.
12. S. Dilip Kumar and P. P. Mondal, Taylor series expansion-based multidimensional image reconstruction for confocal and 4pi microscopy, Appl. Phy. Lett., 103, 073702, 2013.
13. S. Dilip Kumar and P. P. Mondal, Multidimensional data reconstruction for two-color fluorescence microscopy, Review of Scientific Instruments, 82, 063705, 2011.
14. S. Dilip Kumar, A. Diaspro and P. P. Mondal, Spatial filter-based 3D resolution improvement and polarization properties of multiphoton multiple-excitation-spot-optical microscopy, Review of Scientific Instruments, 82, 063705, 2011.
15. S. Dilip Kumar and P. P. Mondal, High resolution multiple excitation spot optical microscopy, AIP Advances 1, 022128, 2011.

SOM Confocal Microscopy Core Facility