SOPi/Crossbill

for more details visit: SOPi and Crossbill

Related publication(s):

Peer-reviewed journals:

1. 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

2. 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

3. 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

4. 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

Patent(s):

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

2. Y. Kozorovitskiy and M. Kumar, "Confidential title - to be announced when public", US patent, 2020/21

Conference:

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, (April 2020). doi: 10.1364/BRAIN.2020.BW4C.5

Non peer-reviewed publications:

1. M. Kumar, and Yevgenia Kozorovitskiy, "Three mirror architecture for tilt invariant lateral scanning", Zenodo (2020) doi: 10.5281/zenodo.3665902

2. M. Kumar, and Yevgenia Kozorovitskiy, "Crossbill Design", Zenodo (2019) doi: 10.5281/zenodo.3543786

Chickadee: A compact low cost light-sheet microscope

This project is focused towards developing a low-cost (< $2000) light-sheet microscope for imaging large cleared biological samples e.g. mouse brain.

Related publication(s):

Conference:
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 (23 February 2018)
doi: 10.1117/12.2288497

Hornbill: A light-sheet microscope with casque?

(coming soon)

During my first postdoctoral position, at University of Michigan, I worked on the problem of imaging through a scattering media. The main approach behind this research was to make use of a modified off-axis holography setup to mitigate the scattering effects and allow for imaging through a scattering media.

We realized an enhanced imaging capability through a scattering layer by a counter-intuitive idea i.e. by introduction of an additional diffuser! When this additional diffuser is moved (rotated), it leads to reduction of the speckle contrast thus improving the imaging capability of the system. The whole system was implemented based on an off-axis holography setup.

Related publication(s):

Journal:

1. 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)

Conference:

1. M. J. Purcell, M. Kumar and S. C. Rand, "Holographic imaging through a scattering medium by diffuser-assisted statistical averaging",
   SPIE OPTO, 97710F, March 2016. (doi: 10.1117/12.2212845)

This was the main research project during my PhD program at IIT Delhi. This research was aimed at making use of a phase only spatial light modulator (SLM) as a phase engineered diffractive element and employ a simple 4F Fourier filtering setup for single step micro-fabrication of various novel photonic crystal structures.

A phase-only Spatial Light Modulator (SLM) can be used to display a phase engineered grating. Phase SLMs are reconfigurable in the sense that a phase pattern can be calculated computationally and then displayed electronically. Therefore, a simple 4F Fourier filtering based optical setup can be employed to generate a range of 2D photonic crystal structures by changing the displayed phase pattern and Fourier mask. This enables a simple single shot micro-fabrication technique for 2D photonic crystal structures.

Experimental steps:

• A numerically calculated 2D grating is displayed on the phase SLM.

• An expanded and collimated laser beam (405 nm) gets diffracted from the SLM to form the far field Fourier intensity pattern in the focal plane of the first converging lens.

• A Fourier filter helps discard unwanted signal and a second converging lens helps performs 2nd Fourier transform operation to form the desired interference pattern in its focal plane.

• Final pattern is either digitally recorded on a Camera or physically recorded in a photo-resist material.

Range of structures micro-fabricated with this approach:

• Single/multiple defect embedded periodic photonic crystal structures

• Gradient fill-fraction photonic crystal structures

• Spatially varying photonic crystal structures

Related code:

I've written a simple jupyter-notebook openly available as a Github repository here: https://github.com/OptoManishK/multi-beam-interference

(The notebook runs with IPython/Jupyter-note/Jupyter-lab and calculates N-beam interference field profile. The code can be used to simulate any combination of multiple beam interference profile, and calculate corresponding phase profile to be displayed on the SLM.

Related publication(s):

Journals:

1. S. Behera, M. Kumar and J. Joseph, "Submicrometer photonic structure fabrication by phase spatial-light-modulator-based interference lithography", Opt. Lett. 41 (8) 1893-1896 (2016)

2. A. Kapoor, M. Kumar, P. Senthilkumaran and J. Joseph, "Optical vortex array in spatially varying lattice", Opt. Commun. 365, 99-102, (2016)

3. M. Kumar and J Joseph, "Optical generation of a spatially variant two-dimensional lattice structure by using a phase only spatial light modulator", Appl. Phys. Lett. 105(5), 051102 (2014)

4. M. Kumar and J Joseph, “Generating a hexagonal lattice wave-field with a gradient basis structure”, Opt. Lett. 39(8), 2459-2462 (2014)

5. 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” Opt. Commun. 322, 160-163 (2014)

6. M. Kumar and J. Joseph, “Digitally reconfigurable complex 2D Dual lattice structure by optical phase engineering”, Appl. Optics 53(6), 1333-1338 (2014)

7. M. Kumar and J. Joseph, "Embedding multiple nondiffracting defect sites in periodic lattice wavefield by optical phase engineering", J. Nanophoton. 8(1), 083894 (2014).

8. M. Kumar and J. Joseph, "Embedding a non-diffracting defect site in helical lattice wave-field by optical phase engineering", Appl. Optics 52, 5653-5658, (2013)

Conferences:

1. M. Kumar and J. Joseph, “Tunable dual-lattice 2D patterns by making use of programmable phase mask”, International conference on optics and optoelectronics, XXXVIII symposium of Optical Society of India, IRDE, Dehradun, 5-8th March 2014

2. M. Kumar and J. Joseph, “Binary phase masks for embedding non-diffracting defect sites in 2D Square lattice wave-field”, Workshop on Recent Advances in Photonics, Indian Institute of Technology Delhi, 17-18th December, 2013 (link)

3. M. Kumar and J. Joseph, “Embedding multiple non-diffracting defect sites in 2D photonic lattice by optical phase engineering”, Focused discussion meeting on Metamaterials and Photonic Nanostructures, Indian Institute of Technology Kanpur, 16-18th August, 2013.

4. M. Kumar and J. Joseph, “Broadband all angle super-collimation in 2D hexagonal hybrid photonic crystal”, XXXVIIth Optical Society of India conference, Pondicherry University, Jan 2013.