Publications – Krishna’s Group

Journals

[J1] K. Agarwal and R. Machan, Multiple Signal Classification Algorithm for super-resolution fluorescence microscopy, Nature Communications, vol. 7, article id. 13752, 2016. (impact factor = 12.124) (Preprint and an easily readable supplement PDF) (PDF)

[J2] K. Agarwal and D.K. Prasad, "Eigen-analysis reveals components supporting super-resolution imaging of blinking fluorophores", Scientific Reports, vol. 7, 2017. (impact factor = 4.259) (Source code)(PDF)

[J3] K. Agarwal, R. Machan, and D. K. Prasad, “Non-heuristic automatic techniques for overcoming low signal-to-noise-ratio bias of localization microscopy and multiple signal classification algorithm”, Scientific Reports, 2018. (impact factor = 4.259)(source code and PDF)

[J4] K. Samanta, J. Joseph, B. S. Ahluwalia, K. Agarwal. "Study of electric fields of diffraction from spatial light modulator: Discussion". Optical Society of America. Journal A: Optics, Image Science, and Vision; Volume 36.(10) p. 1778-1786 (2019) (PDF)

[J5] I. S. Opstad, F. Ströhl, Å. B. Birgisdottir, S. A. Acuña M., T. Kalstad, T. Myrmel, K. Agarwal and B. S. Ahluwalia, “Adaptive fluctuation imaging captures rapid subcellular dynamics”, Proc. SPIE 11076, Advances in Microscopic Imaging II, 110761W (22 July 2019) (PDF)

[J6] S. Acuña M., F. Ströhl, I. S. Opstad, B. S. Ahluwalia and K. Agarwal. “MusiJ: an ImageJ plugin for video nanoscopy.” Biomed. Opt. Express 11, 2548-2559 (2020) (PDF)

[J7] A. Ahmed, I. S. Opstad, Å. B. Birgisdottir, T. Myrmel, B. S. Ahluwalia, K. Agarwal and D. K. Prasad, “Learning nanoscale motion patterns of vesicles in living cells“, IEEE Conference on Computer Vision and Pattern Recognition (CVPR), Seattle, Washington, USA, 16-18, June, 2020.

[J8] F. Ströhl, S. Jadhav, B. S. Ahluwalia, K. Agarwal, and D. K. Prasad, “Object detection neural network improves Fourier ptychography reconstruction,” Opt. Express 28, 37199-37208 (2020) (PDF)

[J9] N. Jayakumar, Ø. I. Helle, K. Agarwal, and B. S. Ahluwalia, "On-chip TIRF nanoscopy by applying Haar wavelet kernel analysis on intensity fluctuations induced by chip illumination," Opt. Express 28, 35454-35468 (2020) (PDF)

[J10] S. Acuña, I. S. Opstad, F. Godtliebsen, B. S. Ahluwalia, and K. Agarwal, "Soft thresholding schemes for multiple signal classification algorithm," Opt. Express 28, 34434-34449 (2020) (PDF)

[J11] L. Zhang, X. Kuiwen, Y. Zhong, and K. Agarwal. “Solving Phaseless Highly Nonlinear Inverse Scattering Problems With Contraction Integral Equation for Inversion.” IEEE Transactions on Computational Imaging 6 (2020): 1106-1116. (PDF)

[J12] F. Ströhl, S. Jadhav, B. S. Ahluwalia, K. Agarwal, and D. K. Prasad, “Object detection neural network improves Fourier ptychography reconstruction,” Opt. Express 28, 37199-37208 (2020). (PDF)

[J13] S. Jadhav, S. Acuña, I. S. Opstad, B. S. Ahluwalia, K. Agarwal, and D. K. Prasad, "Artefact removal in ground truth deficient fluctuations-based nanoscopy images using deep learning," Biomed. Opt. Express 12, 191-210 (2021). (PDF)

Conferences

2021

[C13] S. Acuña, K. Agarwal, "Autothresholding in MUSICAL using non-orthogonal signal-noise separation", URSI GASS 2021, Rome, Italy, 28 August - 4 September 2021.

2020

[C12] A. Ahmed, I. S. Opstad, Å. B. Birgisdottir, T. Myrmel, B. S. Ahluwalia, K. Agarwal, D. K. Prasad, “Learning nanoscale motion patterns of vesicles in living cells“, IEEE Conference on Computer Vision and Pattern Recognition (CVPR), Seattle, Washington, USA, 16-18 June, 2020.

2019

[C11] S. A. A. Maldonado, G. M. A. Mehedi Hussain, F. Godtliebsen, B. S. Ahluwalia, H. P. Ha, D. K. Prasad, K. Agarwal, “Multiple Signal Classification: Challenges on the Route from Millimeter Resolution to Nanometer Resolution”, Progress In Electromagnetics Research Symposium, Rome, 17-20 June, 2019.

[C10] S. A. A. Maldonado, I.-S. Opstad, L. E. V. Hernandez, M. Nystad, M. Aguilera, M. Storflor, C. I. Oie, S. Abel, A. B. Birgisdottir, T. Karstad, D. L. Wolfson, J.-C. Tinguely, T. Myrmel, P. McCourt, T. Johansen, B. S. Ahluwalia, K. Agarwal, “Fluorescence Nanoscopy Using Multiple Signal Classification Algorithm (MUSICAL): From Electromagnetics Inverse Scattering Problem to Optics Inverse Source Problem”, Progress In Electromagnetics Research Symposium, Rome, 17-20 June, 2019.

2018

[C9] I.-S. Opstad, K. Agarwal, D. A. Popova, G. Acharya, P. Basnet, B. S. Ahluwalia, "Live-cell optical nanoscopy of human spermatozoa", Norwegian Electro-optics meeting 2018,Lofoten, Norway, 2–4 May, 2018.

[C8] K. Agarwal, L. E. V. Hernandez, I.-S. Opstad, M. Nystad, Å. B. Birgisdottir, T. Kalstad, T. Myrmel, C. I. Øie, and B. S. Ahluwalia, "High-speed, high resolution, multi-color imaging of living cells and tissues using MUSICAL", SPIE Optics + Photonics 2018, San Diego, California, United States, 19 - 23 August 2018.

[C7] K. Agarwal, I.-S. Opstad, M. Aguilera, M. Storflor, Å. B. Birgisdottir, D. Wolfson, T. Kalstad, S. Abel, T. Myrmel, T. Johansen, and B. S. Ahluwalia, "Breaking the diffraction barrier at high-speed using MUSICAL", Norwegian Electro-optics meeting 2018,Lofoten, Norway, 2–4 May, 2018.

[C6] K. Agarwal, I.S. Opstad, J.C. Tinguely, S. Abel, T. Kalstad, A.B. Birgisdottir, T. Myrmel, B.S. Ahluwalia, "High-Speed, Multi-Color Live Cell Nanoscopy Using Musical", Focus on Microscopy Conference, Singapore, 25-28 March, 2018.

[C5] Ø. I. Helle, J.-C. Tinguely, D. A. Coucheron, F. Dullo, C. I. Øie, K. Agarwal, B. S. Ahluwalia , "Photonic Chip-Based Multi-Modality TIRF Nanoscopy Platform", Focus on Microscopy Conference, Singapore, 25-28 March, 2018.

2017

[C4] K. Agarwal, Ø. I. Helle, T.D. Firehun, J.-C. Tinguely , and B. S. Ahluwalia, “ Low toxicity super-resolution imaging at high temporal speed using chip-based speckle-MUSICAL suitable for live cell imaging”, EMBL Symposia- Seeing is Believing - Imaging the Processes of Life, Heidelberg, Germany, 4-7 October, 2017.

[C3] K. Agarwal, B. Ghosh, D. L. Wolfson, C. I. Oie, J. Chatterjee, and B. S. Ahluwalia, “Computational Nanoscopy Using Multiple Signal Classification Algorithm (MUSICAL) for Fluorescence Imaging”, Progress In Electromagnetics Research Symposium, Singapore, 19-22 November, 2017.

[C2] I. S. Opstad, S. Abel, B. S. Ahluwalia, and K. Agarwal, “ Multi-color nanoscopy of live-cell processes in E. coli bacteria using MUSICAL”, Progress In Electromagnetics Research Symposium, Singapore, 19-22 November, 2017.

[C1] K. Agarwal, “Multiple Signal Classification: From Millimeter Resolution to Nanometer Resolution”, Progress In Electromagnetics Research Symposium, Singapore, 19-22 November, 2017.

This is where you can find datasets, source code and plugins of our group.

MUSICAL Dataset

Link

MUSICAL ImageJ Plugins

ImageJ Plugin link

The ImageJ Plugin video - How to use JMUSICAL - https://www.youtube.com/watch?v=CsJHqSQb11E

MUSICAL Matlab code?

Source Code of MUSICAL in MATLAB

The video: https://www.youtube.com/watch?v=deCu_tXoIoY

The code usage: https://www.youtube.com/watch?v=k3A5al8AGG4

Speckle MUSICAL

in progress.