OSE Seminar by Prof. Tonmoy Chakraborty on Imaging for physiologically relevant 3D micro-environment

Departmental News

Prof. Tonmoy Chakraborty

Posted: October 27, 2020

Date: Thursday, October 29, 2020 

Time:  12:15 PM to 1:15 PM

Location:  via Zoom

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Biological tissues are composed of multiple cell types organized in a complex three-dimensional architecture.  However, because of the limited penetration depth of visible photons, observing the molecular and structural composition of intact tissues remains challenging. 

By chemically clearing a tissue or an organ, the depth over which an optical microscope can deliver an image is dramatically increased. However, because a large variety of tissue clearing methods exist, each optimized for different types of samples that necessitate specific solvents, imaging with sub-cellular resolution has remained out of reach. In the first part of this presentation, I will talk about my postdoctoral research where I developed a microscopy platform that can image large specimens such as an entire mouse brain or kidney with high resolution, irrespective of the clearing protocol. Also, unlike any other microscope, our system achieves isotropic resolution (i.e. the same resolving power in any spatial direction). Owing to its high-speed, our microscope can image specimens within hours that previously required days to weeks of imaging time. I will also show how various researchers across many different biological fields (neuroscience, stem-cell and cancer research, developmental biology etc.) are using this platform to address their biological questions.  

Observing cells in tissue is to some degree is also possible with multiphoton microscopy. However, due to its raster scanning nature, such microscopes are notoriously slow. Scanning in the third dimension is especially slow, as a change of focus is traditionally achieved by mechanically moving heavy optical components. Here I will present a new optical method that can convert any lateral scan motion into an axial scan while avoiding spherical aberrations. I will demonstrate the potential of this technique by using normal and resonant galvanometric scanners to achieve high resolution axial refocusing at a rate of up to 12kHz. I will discuss how this technology can obtain even faster scan rates in the MHz range and how this will impact intravital imaging using multiphoton microscopy.


The long-term goal of my research is to develop transformative microscope technologies that have an impact in biological research, particularly, in the study of human diseases. I envision myself spearheading a research group which focuses on development of light-sheet and multi-photon imaging modalities.

After gaining several years of microscopy experience in semiconductor industry, as Analytical and Metrology Engineer, I transitioned into my doctoral research through the laboratory of Dr. Jonathan Petruccelli at the State University of New York at Albany. In his lab, I used adaptive optics based techniques to develop a fully automatic setup which could render invisible samples visible, by measuring their quantitative phase (Chakraborty et al. Optics Express 2017, Applied Optics 2018).

Thereafter, I moved to UTSW to hone my skills in microscopy development and design and importantly to immerse myself in an environment of biomedical researchers to ensure that my designs and tool building is guided by the needs and problems of biology. I was successful in developing the highest XYZ resolution light-sheet microscope for millimeter-scale cleared-tissues which can also image, at orders of magnitude, faster than any of its confocal or light-sheet counterparts (Chakraborty et al. Nature Methods 2019). As a testament to the value of this work, the microscope has already generated over ten multidisciplinary collaborations where it is being extensively used by neuro-, cell-and developmental biologists across campus and I already built two of these to meet the growing demand. In addition, two pilot grants based upon this work are well in their advanced stages. More recently, I have developed an inexpensive and fast way of extending the depth of focus of any 2-photon microscope which, I believe, will have a significant impact in ultra-fast imaging of live-cells in bio mimetic models and neuronal activity in brain (Chakraborty & Chen et al. Light: Science & Applications 2020).

Overall, I feel that the field of microscopy is going through rapid changes and constantly paving new roads for biomedical community and I am hopeful that the cutting edge optical platforms that I develop at University of New Mexico will serve pivotal role in upcoming biomedical discoveries.