Manish Kumar

About

Manish is a multidisciplinary researcher who has held positions in Physics, EECS, and Neurobiology. His entire research career has been tied together by Optics. He leads the BIOS research laboratory in SeNSE at IIT Delhi. His research lab focuses on two areas:

1. bio-imaging, and
2. optical systems.

Research interests

Funding

• New Faculty Seed Grant, IIT Delhi (2022-23)
• SERB Startup Research Grant (2023-25)
• Equipment Matching Grant, IIT Delhi (2023-23)

Education & Work Experience

• Jan 2022 - Present: Assistant Professor, SeNSE, IIT Delhi, India
• Aug 2016 - Dec 2021: Post-doc, Neurobiology, Northwestern University, USA
• Jan 2015 - Jul 2016: Post-doc, EECS, University of Michigan, USA
• Aug 2012 - Sep 2012: Visiting Scholar, EIIRIS, Toyohshi University of Technology, Japan
• Jun 2011 - Feb 2016: Ph.D. Physics (Optics)*, IIT Delhi, India
• Jul 2009 - May 2011: M.Tech. Applied Optics, IIT Delhi, India
• Jun 2007 - Apr 2009: M.Sc. Physics, Sri Sathya Sai Institute of Higher Learning, India
• Jun 2004 - Apr 2007: B.Sc. Physics, Sri Sathya Sai Institute of Higher Learning, India

Awards / Fellowships

• Young Faculty Incentive Fellowship, IIT Delhi, 2022-2024
• Senior Research Fellowship (SRF), CSIR , Govt. of India, 2011-2014
• Junior Research Fellowship (JRF), CSIR , Govt. of India, 2009-2011
• MHRD Fellowship, Govt. of India, 2009

Invited Talks

• March 2024: "Remote focusing light-sheet microscopy", Prof. M. K. Sundaresan Memorial Lecture Series, Recent Trends in Photonics, Department of Physics, Sri Sathya Sai Institute of Higher Learning, India
• March, 2022: "Crossbill: a single objective light-sheet microscopy platform for everyone", Practical Technologies Workshop Series, University of Cambridge, UK
• May, 2020: "Light-sheet microscopy goes single objective", Emerging Imaging Technology in Biomedical Research, Mini Symposium, Evanston, IL, USA
• February, 2020: "Scanned Oblique Plane Illumination Microscopy", Cell & Developmental Biology Department at Northwestern University, Chicago, IL, USA
• June, 2019: "Scanned Oblique Plane Illumination Microscopy" Sculpted Light in the Brain Conference, The Royal Society, London, UK
• March, 2019: "Fast 3D imaging with single objective light-sheet microscopy", Midwest Microscopy and Microanalysis Society Spring Meeting, Evanston, IL, USA

Reviewing Experience

• Optica publishing group: Applied Optics, Optics Letters, Optics Express, Biomedical Optics Express, Optics Continuum
• Elsevier: Optics Communications
• Nature publishing group: Scientific Reports, Nature Methods

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• Publications

News

• 04/2024. A first from our lab! Pocket Schlieren preprint is out here. Thanks to Diganta for a great work.
• 03/2024. Manish gives an invited talk at Sri Sathya Sai Institute of Higher Learning (Anantpur, India).
• 07/2023. Akshay Kumar joins lab under the SeNSE Ph.D. program. Welcome to the lab.
• 06/2023. Diganta Rabha joins lab as lab's first post-doc. Welcome to the lab.
• 02/2023. Manish secures SERB SRG research grant for exploring microscopy.
• 01/2023. Dinesh Saini joins lab under the OPC Ph.D. program. Welcome to the lab.
• 10/2022. Manish given an invited (in person) talk at UiT | The Arctic University of Norway.
• 08/2022. Vimod Kumar joins lab under the SeNSE Ph.D. program. Welcome to the lab.
• 07/2022. Manish joins the SCOPE22 initiative from OPC (Optics and Photonics Centre) at IIT Delhi.
• 04/2022. Neeraj Joshi, Piyush Jain and Shubham Saxena join BIOS lab for their M.Tech projects. Welcome to the lab.
• 03/2022. Manish gives an invited (virtual) talk at a workshop series organized under Engineering Biology at the University of Cambridge
• 01/2022. Manish joins in SeNSE.

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People

Faculty

• Manish Kumar more info

Post-doc

• Diganta Rabha, Institute post-doc, SeNSE, Jun 2023 - present

Ph.D.

• Akshay Kumar (2023IDZ8182), SeNSE, Jul 2023 - present
• Dinesh Saini (2022OPZ8594), OPC, Jan 2023 - present
• Vimod Kumar (2022IDZ8389), SeNSE, Jul 2022 - present

M.Tech.

• Apoorv Ranjan, M.Tech. (Instrument Technology), 2022-24
• Kapil Chauhan, M.Tech. (Instrument Technology), 2022-24

Others

• Yashika Mehta, SCOPE'23

Past members

• Shubham Saxena, M.Tech. (Applied Optics), 2021-23 and SCOPE'22 (Now Research Scholar abroad)
• Vivek Jha, SCOPE'22 (Now Optical Engineer at BioTech Vision Care)
• Neeraj Joshi, M.Tech. (Instrument Technology), 2021-23 (Now with TVS Motor)
• Piyush Jain, M.Tech. (Instrument Technology), 2021-23 (Now with Tech Mahindra)

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Teaching

Academic year 2023-24:

Sem I

Sem II

Academic year 2022-23:

Sem I

Sem II

Academic year 2021-22:

Sem II

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Research

Intro

Current Research Areas

1. Optical microscopy

2. Schleiren imaging

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• Publications

Publications

Profiles: Google Scholar | IRINS

Patent(s)

1. Y. Kozorovitskiy and M. Kumar, "Scanned oblique plane illumination microscopy", US Patent 10802255 (2020)
2. Y. Kozorovitskiy and M. Kumar, "Low numerical aperture lens based oblique plane illumination imaging", World Patent WO2020159931A1 (2020)

Pre-print

1. 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 articles

1. 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 12 , 4855 (2021) doi: 10.1038/s41467-021-25144-y
2. 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 39, 368–377 (2021) doi: 10.1038/s41587-020-0710-1
3. 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
4. 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
5. 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) [Highlighted as Editor's pick] doi: 10.1364/OE.26.013027
6. M. J. Purcell, M. Kumar, S. C. Rand and V. Lakshminarayanan, "Holographic imaging through a scattering medium by diffuser-aided statistical averaging", JOSA A 33 (7) 1291-1297 (2016) doi: 10.1364/JOSAA.33.001291
7. S. Behera, M. Kumar and J. Joseph, "Submicrometer photonic structure fabrication by phase spatial-light-modulator-based interference lithography", Optics Letters 41 (8) 1893-1896 (2016) doi: 10.1364/OL.41.001893
8. A. Kapoor, M. Kumar, P. Senthilkumaran and J. Joseph, "Optical vortex array in spatially varying lattice", Optics Communications 365, 99-102, (2016) doi: 10.1016/j.optcom.2015.11.074
9. M. Kumar and J. Joseph, "Optical generation of a spatially variant two-dimensional lattice structure by using a phase only spatial light modulator", Applied Physics Letters 105 (5), 051102 (2014) doi: 10.1063/1.4892447
10. M. Kumar and J Joseph, “Generating a hexagonal lattice wave-field with a gradient basis structure”, Optics Letters 39(8), 2459-2462 (2014) doi: 10.1364/OL.39.002459
11. S. Raghuraman, M. Kumar, J. Joseph, and M. V. Matham “Realization of body centered tetragonal, β-tin and diamond type structures using five beam interference” Optics Communications 322, 160-163 (2014) doi: 10.1016/j.optcom.2014.02.038
12. M. Kumar and J. Joseph, “Digitally reconfigurable complex 2D Dual lattice structure by optical phase engineering”, Applied Optics 53(6), 1333-1338 (2014) doi: 10.1364/AO.53.001333
13. M. Kumar and J. Joseph, "Embedding multiple nondiffracting defect sites in periodic lattice wavefield by optical phase engineering", Journal of Nanophotonics 8(1), 083894 (2014) doi: 10.1117/1.JNP.8.083894
14. M. Kumar and J. Joseph, "Embedding a non-diffracting defect site in helical lattice wave-field by optical phase engineering", Applied Optics 52(23), 5653-5658, (2013) doi: 10.1364/AO.52.005653
15. M. Kumar, R. Jindal and J. Joseph, "FDTD modeling based comparison of RIE based and Sol-gel based PC-OLED devices", Journal of Optics 41, 243-250 (2012) doi: 10.1007/s12596-012-0088-7
16. R. Gowrishankar, M. Kumar, V. Menon, S. M. Divi, M. Saravanan, P. Magudapathy, B. K. Panigrahi, K. G. M. Nair and K. Venkataramaniah, "Trace Element Studies on Tinospora cordifolia (Menispermaceae), Ocimum sanctum (Lamiaceae), Moringa oleifera (Moringaceae), and Phyllanthus niruri (Euphorbiaceae) Using PIXE", Biological Trace Element Research 133, 357-363 (2010) doi: 10.1007/s12011-009-8439-1

Conference articles (partial list)

1. M. Kumar and Y. Kozorovitskiy, "Making oblique light-sheet platform open", Optics and the Brain, Biophotonics Congress: Biomedical Optics 2020, Optical Society of America, Washington, DC , USA (April 2020). doi: 10.1364/BRAIN.2020.BW4C.5
2. M. Kumar, J. Nasenbeny and Y. Kozorovitskiy, "Low cost light-sheet microscopy for whole brain imaging", Proc. SPIE 10499, Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXV, 104991I, San Francisco, CA, USA (23 February 2018) doi: 10.1117/12.2288497
3. M. J. Purcell, M. Kumar and S. C. Rand, "Holographic imaging through a scattering medium by diffuser-assisted statistical averaging" SPIE OPTO, 97710F, San Francisco, CA, USA (March 2016) doi: 10.1117/12.2212845

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Resources

In here you will find some helpful resources from our lab.

Pocket Schlieren

Openhouse 2023

1. BIOS lab research overview (Download File)
2. Schlieren imaging systems (Download File)
3. Infosheet for Background Oriented Schlieren (BOS) imaging (Download File)

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Contact

Office:
3B - 21 (Block III)
coming soon!
kmanish[at]iitd[dot]ac[dot]in

Lab:
WS - 212, WS - 214 (SeNSE)

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Elements

i = 0;

while (!deck.isInOrder()) {
    print 'Iteration ' + i;
    deck.shuffle();
    i++;
}

print 'It took ' + i + ' iterations to sort the deck.';