This website is not updated anymore! Manish has moved to IIT Delhi (India) and his new website link is : https://web.iitd.ac.in/~kmanish

Hi, I'm a postdoctoral scholar at Northwestern University, USA.

I perform interdisciplinary research focused around optics. My current research involves developing advanced light-sheet microscopy techniques for biological imaging. I've also worked in the fields of holographic imaging and interference lithography.

My broad research interest lies in developing valuable optical technologies and making them accessible.

I joined Prof. Kozorovitskiy's lab at Northwestern University to build a conventional light-sheet microscope for imaging neurons. This was a new field for me and I was soon fascinated by the open-source development of this class of microscopes by multiple research groups. Backed with my strong training in optics, I quickly realized a technical flaw with then scanning geometry in single objective light-sheet microscopy approach. This made me one of the leading researchers in this field.

I invented single planar mirror enabled geometry to produce tilt-invariant lateral scan for rapid 3D imaging. A continued advancement through improved hardware and software development of this Scanned Oblique Plane Illumination (SOPi) microscopy technique has become by primary research focus.

Key features of SOPi: Blazing fast 3D imaging (>10 times faster than confocal), steric access (single objective facing sample), multi-photon imaging (>10 times faster than point-scanning 2p imaging), multi-color imaging, low phototoxicity, GECI/GEVI imaging (through depth in bulk tissue/living specimen), etc.

My résumé ...

Research

Light-sheet microscopy

Postdoctoral research
Northwestern University
(2016-present)

Holographic imaging

Pre/post-doctoral research
University of Michigan
(2015-2016)

Interference lithography

Doctoral research
IIT Delhi
(2011-2015/16)

More research ...

Recent publications

Pre-print(s):

M. Kumar, S. Kishore, D. McLean and Y. Kozorovitskiy, "Crossbill: an open access single objective light-sheet microscopy platform", bioRxiv (2021)
doi: 10.1101/2021.04.30.442190

Journal(s):

V. Dumrongprechachan, R. B. Salisbury, G. Soto, M. Kumar, M. L. MacDonald, and Y. Kozorovitskiy, "Cell-type and subcellular compartment-specific APEX2 proximity labeling reveals activity-dependent nuclear proteome dynamics in the striatum", Nature Communications (2021)
doi: 10.1038/s41467-021-25144-y

A. A. Shemetov, M. V. Monakhov, Q. Zhang, J. E. Canton-Josh, M. Kumar, M. Chen, M. E. Matlashov, X. Li, W. Yang, L. Nie, D. M. Shcherbakova, Y. Kozorovitskiy, J. Yao, N. Ji, and V. V. Verkhusha, "A near-infrared genetically encoded calcium indicator for in vivo imaging", Nature Biotechnology (2020)
doi: 10.1038/s41587-020-0710-1

M. Kumar, and Y. Kozorovitskiy, "Tilt (in)variant lateral scan in oblique plane microscopy: a geometrical optics approach",
Biomedical Optics Express, 11 (6), 3346-3359 (2020)
doi: 10.1364/BOE.389654

M. Kumar, and Y. Kozorovitskiy, "Tilt-invariant scanned oblique plane illumination microscopy for large-scale volumetric imaging",
Optics Letters, 44 (7), 1706-1709 (2019)
doi: 10.1364/OL.44.001706

M. Kumar, S. Kishore, J. Nasenbeny, D. McLean and Y. Kozorovitskiy, "Integrated one- and two-photon scanned oblique plane illumination (SOPi) microscopy for rapid volumetric imaging",
Optics Express, 26 (10), 13027-13041 (2018)
doi: 10.1364/OE.26.013027 [Highlighted as Editor's pick]

Patent(s):

Y. Kozorovitskiy and M. Kumar, "Scanned oblique plane illumination microscopy", US patent number 10802255 (2020)

More publications ...

Visual research highlights

Zebrafish_10vps.mp4

Multi-plane functional imaging

Zebrafish under visual stimulus, 10 planes imaged at 10 Hz each

More details

DSOPi_thy1GFP.mp4

Large volume light-sheet microscopy

Mouse brain section, uncleared, imaging time ~20 seconds (dataset)

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News and Announcements

Aug 2021: A collaborative paper using Crossbill microscope is published in Nature Communications. Read the paper here: https://rdcu.be/ctRIn
July 2021: A dataset for single objective light-sheet acquired large volume is public on zenodo here.
May 2021: Crossbill pre-print is live here.
March 2021: "Trishanku: a collimation tester for less than 1 cent" is posted here.
Jan 2021: Crossbill website is soon going public here.
Oct 2020: SOPi is granted and published as a US patent. Read the document here: US10802255B2
Oct 2020: A collaborative paper showing SOPi microscopy application is published in Nature Biotechnology. Read paper here: https://rdcu.be/b9dbq
May 2020: New SOPi publication in Biomedical Optics Express (link)
Feb 2020: A reflection mode SOPi scanner design is available at 10.5281/zenodo.3665902.
Nov 2019: Crossbill Design: a GUI to design single objective light-sheet microscope is openly accessible at 10.5281/zenodo.3543786
June 2019: Presented a short talk during SLB 2019 conference at the Royal Society, London. Few slides are openly accessible here.

March 2019: SOPi v2.0 paper is published in Optics Letters 10.1364/OL.44.001706
March 2019: Presented an invited talk at Midwest Microscopy and Microanalysis Society Spring Meeting.
Jan 2019: New SOPi preprint is available here.
July 2018: Northwestern University TGS covered me in their spotlight story here (link inactive - last checked Sep 2020).
May 2018: SOPi (read as So - π) is published as an Editor's pick in Optics Express 10.1364/OE.26.013027
April 2018: SOPi preprint is available here.
Feb 2018: Our $2000 light-sheet microscope (project chickadee) is out here.
Jan 2018: Great time spent at SPIE Photonics West. (Oral presentation)

Contact

Work Address:

Kozorovistkiy Lab,
Room 2325, Pancoe Life Sciences Pavilion,
2200 Campus Drive, Evanston, IL 60208, USA
Phone: +1 (847) 491 8358 , Email: (see footer)

Mailing Address:

The Department of Neurobiology
Northwestern University
2205 Tech Drive, Hogan 2-160
Evanston, IL 60208, USA

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