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Label-free 3D morphological nanoscopy for studying sub-cellular dynamics in live cancer cells with high spatio-temporal resolution

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Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Other (5)
Guiding Artificial Intelligence Through Physics for Scientific Problems

Author(s): Krishna Agarwal
Published in: IEEE SPS Webinar, 2024
Publisher: IEEE

Label-free chip-based evanescent light scattering super-resolution and superior-contrast optical microscopy (cELS) (opens in new window)

Author(s): Jayakumar, Nikhil; Dullo, Firehun T; Dubey, Vishesh; Ahmad, Azeem Ahmad; Cauzzo, Jennifer; Guerreiro, Eduarda Mazagao; Snir, Omri; Skalko-Basnet, Natasa; Agarwal, Krishna; Ahluwalia, Balpreet Singh
Published in: Arxiv, Issue 1, 2021
Publisher: Arxiv
DOI: 10.48550/arxiv.2108.10575

Fluorescence fluctuations-based super-resolution microscopy techniques: an experimental comparative study (opens in new window)

Author(s): Opstad, Ida S.; Acu��a, Sebastian; Hernandez, Lu��s Enrique Villegas; Cauzzo, Jennifer; ��kalko-Basnet, Nata��a; Ahluwalia, Balpreet S.; Agarwal, Krishna
Published in: Arxiv, Issue 1, 2021
Publisher: Arxiv
DOI: 10.48550/arxiv.2008.09195

tAF-MUSICAL: Autofluorescence Super-resolution Microscopy for Molecular Histopathology of Matrix Proteins in Fibrotic Diseases (opens in new window)

Author(s): Biswajoy Ghosh, Jyotirmoy Chatterjee, Ranjan Paul, Pooja Lahiri, Mousumi Pal, Pabitra Mitra, Balpreet Singh Ahluwalia, Krishna Agarwal
Published in: 2024
Publisher: Springer Science and Business Media LLC
DOI: 10.21203/rs.3.rs-101219/v1

High-resolution imaging in acoustic microscopy using deep learning (opens in new window)

Author(s): Pragyan Banerjee, Shivam Milind Akarte, Prakhar Kumar, Muhammad Shamsuzzaman, Krishna Agarwal , Ankit Butola,Dilip K. Prasad, Frank Melandsø, and Habib Anowarul
Published in: Researchsquare pre-print, 2022
Publisher: Researchsquare
DOI: 10.21203/rs.3.rs-1669440/v1

Peer reviewed articles (24)
Soft thresholding schemes for multiple signal classification algorithm (opens in new window)

Author(s): Sebastian Acuña, Ida S. Opstad, Fred Godtliebsen, Balpreet Singh Ahluwalia, Krishna Agarwal
Published in: Optics Express, Issue 28/23, 2020, Page(s) 34434, ISSN 1094-4087
Publisher: Optical Society of America
DOI: 10.1364/oe.409363

Deriving high contrast fluorescence microscopy images through low contrast noisy image stacks (opens in new window)

Author(s): Sebastian Acuña, Mayank Roy, Luis E. Villegas-Hernández, Vishesh K. Dubey, Balpreet Singh Ahluwalia, and Krishna Agarwal
Published in: Biomedical Optics Express, Issue 12/9, 2021, Page(s) 5529-5543, ISSN 2156-7085
Publisher: The Optical Society
DOI: 10.1364/boe.422747

Physics-based machine learning for subcellular segmentation in living cells (opens in new window)

Author(s): Arif Ahmed Sekh, Ida S. Opstad, Gustav Godtliebsen, Åsa Birna Birgisdottir, Balpreet Singh Ahluwalia, Krishna Agarwal & Dilip K. Prasad
Published in: Nature Machine Intelligence, Issue 3, 2021, Page(s) 1071–1080, ISSN 2522-5839
Publisher: Springer Nature
DOI: 10.1038/s42256-021-00420-0

Computational Comparison and Validation of Point Spread Functions for Optical Microscopes (opens in new window)

Author(s): Zicheng Liu, Yingying Qin, Jean-Claude Tinguely, Krishna Agarwal
Published in: IEEE Transactions on Computational Imaging, Issue 11, 2025, Page(s) 170-178, ISSN 2333-9403
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/tci.2025.3536106

Multimodal on-chip nanoscopy and quantitative phase imaging reveals the nanoscale morphology of liver sinusoidal endothelial cells (opens in new window)

Author(s): Ankit Butola, David A Coucheron, Karolina Szafranska, Azeem Ahmad, Hong Mao, Jean-Claude Tinguely, Peter McCourt, Paramasivam Senthilkumaran, Dalip Singh Mehta, Krishna Agarwal, Balpreet Singh Ahluwalia
Published in: Proceedings of the National Academy of Sciences, Issue 118/47, 2021, ISSN 1091-6490
Publisher: National Academy of Science
DOI: 10.1073/pnas.2115323118

Taxonomy of hybridly polarized Stokes vortex beams (opens in new window)

Author(s): Arora, Gauri; Butola, Ankit; Rajput, Ruchi; Agarwal, Rohit; Agarwal, Krishna; Horsch, Alexander; Prasad, Dilip K; Senthilkumaran, Paramasivam
Published in: Optics Express, Issue 1, 2024, ISSN 1094-4087
Publisher: Optical Society of America
DOI: 10.48550/arxiv.2306.05974

Blind Super-Resolution Approach for Exploiting Illumination Variety in Optical-Lattice Illumination Microscopy (opens in new window)

Author(s): Krishnendu Samanta; Swagato Sarkar; Swagato Sarkar; Sebastian Acuña; Joby Joseph; Balpreet Singh Ahluwalia; Krishna Agarwal
Published in: ACS Photonics, Issue 1, 2021, ISSN 2330-4022
Publisher: American Chemical Society
DOI: 10.1021/acsphotonics.1c00503

Virtual labeling of mitochondria in living cells using correlative imaging and physics-guided deep learning (opens in new window)

Author(s): Ayush Somani; Arif Ahmed Sekh; Ida S. Opstad; Åsa Birna Birgisdottir; Truls Myrmel; Balpreet Singh Ahluwalia; Alexander Horsch; Krishna Agarwal; Dilip K. Prasad
Published in: Biomed Opt Express, Issue 4, 2022, ISSN 2156-7085
Publisher: The Optical Society
DOI: 10.1364/boe.464177

On-chip TIRF nanoscopy by applying Haar wavelet kernel analysis on intensity fluctuations induced by chip illumination (opens in new window)

Author(s): Nikhil Jayakumar, Øystein I. Helle, Krishna Agarwal, Balpreet Singh Ahluwalia
Published in: Optics Express, Issue 28/24, 2020, Page(s) 35454, ISSN 1094-4087
Publisher: Optical Society of America
DOI: 10.1364/oe.403804

Characterizing the consistency of motion of spermatozoa through nanoscale motion tracing (opens in new window)

Author(s): Sunil Bhatt, Ankit Butola, Sebastian Acuña, Daniel Henry Hansen, Jean-Claude Tinguely, Mona Nystad, Dalip Singh Mehta, Krishna Agarwal
Published in: F&S Science, Issue 5, 2024, Page(s) 215-224, ISSN 2666-335X
Publisher: Elsevier BV
DOI: 10.1016/j.xfss.2024.07.002

Physics-Guided Loss Functions Improve Deep Learning Performance in Inverse Scattering (opens in new window)

Author(s): Zicheng Liu, Mayank Roy, Dilip K. Prasad, Krishna Agarwal
Published in: IEEE Transactions on Computational Imaging, Issue 8, 2024, Page(s) 236-245, ISSN 2333-9403
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/tci.2022.3158865

Scalable-resolution structured illumination microscopy (opens in new window)

Author(s): Ankit Butola; Sebastian Acuna; Daniel Henry Hansen; Krishna Agarwal
Published in: Optics Express, Issue 1, 2022, ISSN 1094-4087
Publisher: Optical Society of America
DOI: 10.1364/oe.465303

Fluorescence microscopy and correlative brightfield videos of mitochondria and vesicles in H9c2 cardiomyoblasts (opens in new window)

Author(s): Ida S. Opstad, Åsa B. Birgisdottir, Krishna Agarwal
Published in: Scientific Data, Issue 11, 2024, ISSN 2052-4463
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s41597-024-02970-5

Object detection neural network improves Fourier ptychography reconstruction (opens in new window)

Author(s): Florian Ströhl, Suyog Jadhav, Balpreet S. Ahluwalia, Krishna Agarwal, Dilip K. Prasad
Published in: Optics Express, Issue 28/25, 2020, Page(s) 37199, ISSN 1094-4087
Publisher: Optical Society of America
DOI: 10.1364/oe.409679

MusiJ: an ImageJ plugin for video nanoscopy (opens in new window)

Author(s): Sebastian Acuña, Florian Ströhl, Ida S. Opstad, Balpreet S. Ahluwalia, Krishna Agarwal
Published in: Biomedical Optics Express, Issue 11/5, 2020, Page(s) 2548, ISSN 2156-7085
Publisher: The Optical Society
DOI: 10.1364/boe.382735

Single-shot multispectral quantitative phase imaging of biological samples using deep learning (opens in new window)

Author(s): Sunil Bhatt, Ankit Butola, Anand Kumar, Pramila Thapa, Akshay Joshi, Suyog Jadhav, Neetu Singh, Dilip K. Prasad, Krishna Agarwal, Dalip Singh Mehta
Published in: Applied Optics, Issue 62, 2024, Page(s) 3989, ISSN 1559-128X
Publisher: Optica Publishing Group
DOI: 10.1364/ao.482788

Artefact removal in ground truth deficient fluctuations-based nanoscopy images using deep learning (opens in new window)

Author(s): Suyog Jadhav, Sebastian Acuña, Ida S. Opstad, Balpreet Singh Ahluwalia, Krishna Agarwal, Dilip K. Prasad
Published in: Biomedical Optics Express, Issue 12/1, 2021, Page(s) 191, ISSN 2156-7085
Publisher: The Optical Society
DOI: 10.1364/boe.410617

PyQPI: Open source python framework for the reconstruction of off-axis quantitative phase imaging (opens in new window)

Author(s): Ankit Butola, Sigurd Hellberg, Hong Mao, Krishna Agarwal
Published in: Optics & Laser Technology, Issue 181, 2024, Page(s) 111606, ISSN 0030-3992
Publisher: Elsevier BV
DOI: 10.1016/j.optlastec.2024.111606

Analyzing Mitochondrial Morphology Through Simulation Supervised Learning (opens in new window)

Author(s): Krishna Agarwal; Alexander Horsch; Dilip K. Prasad; Åsa Birna Birgisdottir; Sebastian Andres Acuna Maldonado; Ayush Somani; Gustav Godtliebsen; Abhinanda Ranjit Punnakkal
Published in: Optics Express, Issue 1, 2022, ISSN 1094-4087
Publisher: Optical Society of America
DOI: 10.3791/64880-v

Molecular histopathology of matrix proteins through autofluorescence super-resolution microscopy (opens in new window)

Author(s): Biswajoy Ghosh, Jyotirmoy Chatterjee, Ranjan Rashmi Paul, Sebastian Acuña, Pooja Lahiri, Mousumi Pal, Pabitra Mitra, Krishna Agarwal
Published in: Scientific Reports, Issue 14, 2024, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-024-61178-0

Silicon substrate significantly alters dipole-dipole resolution in coherent microscope (opens in new window)

Author(s): Zicheng Liu, Krishna Agarwal
Published in: Optics Express, Issue 28/26, 2020, Page(s) 39713, ISSN 1094-4087
Publisher: Optical Society of America
DOI: 10.1364/oe.409629

Multi-moded high-index contrast optical waveguide for super-contrast high-resolution label-free microscopy (opens in new window)

Author(s): Nikhil Jayakumar; Firehun T. Dullo; Vishesh Dubey; Azeem Ahmad; Florian Ströhl; Jennifer Cauzzo; Eduarda Mazagao Guerreiro; Omri Snir; Natasa Skalko-Basnet; Krishna Agarwal; Balpreet Singh Ahluwalia
Published in: Nanophotonics, Issue 2, 2022, ISSN 2330-4022
Publisher: American Chemical Society
DOI: 10.1515/nanoph-2022-0100

Single-shot multispectral quantitative phase imaging using deep neural network (opens in new window)

Author(s): Bhatt, Sunil; Butola, Ankit; Kumar, Anand; Thapa, Pramila; Joshi, Akshay; Singh, Neetu; Agarwal, Krishna; Mehta, Dalip Singh
Published in: Applied Optics, Issue 1, 2023, ISSN 1559-128X
Publisher: Optica
DOI: 10.48550/arxiv.2201.01517

3D refractive index reconstruction from phaseless coherent optical microscopy data using multiple scattering-based inverse solvers—a study (opens in new window)

Author(s): Yingying Qin; Ankit Butola; Krishna Agarwal
Published in: Inverse Problems, Issue 1, 2024, ISSN 0266-5611
Publisher: Institute of Physics Publishing
DOI: 10.1088/1361-6420/ad0c29

Conference proceedings (29)
Shape based forward solver for multi-nested body in label-free microscopy”, Focus on Microscopy

Author(s): Yi Huang, Yingying Qin, Krishna Agarwal
Published in: Focus on Microscopy, 2025, 2025
Publisher: Focus on Microscopy

Live measurement of cancel cell motility and plasticity by label-free imaging of intracellular actin dynamics using gradient light interference microscopy

Author(s): Biswajoy Ghosh, Krishna Agarwal
Published in: Focus on Microscopy, 2025, 2025
Publisher: Focus on Microscopy

Quantitative phase imaging for tracing the motion of waveguide trapped bead particle

Author(s): Sunil Bhatt, Ankit Butola, Sebastian Acuña, Daniel Henry Hansen, Jean-Claude Tinguely, Dalip Singh Mehta, Balpreet Singh Ahluwalia, and Krishna Agarwal
Published in: Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XXI, 2023
Publisher: SPIE

Blind reconstruction of challenging raw data outperforms commercial 3DSIM

Author(s): I.S. Opstad, S. Acuña, S. Ströhl, F. Ströhl, B.S. Ahluwalia, K. Agarwal
Published in: Focus on Microscopy, 2023
Publisher: Focus on Microscopy

Adaptation and performance of well known non-linear inverse solvers in optical microscopy

Author(s): Yingying Qin, Ankit Butola, Krishna Agarwal
Published in: Photonics and Electromagnetics Research Symposium, 2024
Publisher: PIERS

Multiscale resolution in Structured illumination microscopy

Author(s): A. Butola, S. Acuna, D.H. Hansen, K. Agarwal
Published in: Focus on Microscopy, 2023
Publisher: Focus on Microscopy

Reconstruction of objects at cell scale from microscope images with inverse scattering algorithm

Author(s): Yingying Qin, Yu Zhong and Krishna Agarwal
Published in: International Conference on Electromagnetics in Advanced Applications, Issue ICEAA – IEEE APWC 2025, 2026
Publisher: IEEE

Enhancing and exploiting multiple scattering in label-free microscopy

Author(s): Krishna Agarwal
Published in: Norwegian Biophysics Symposium, 2024
Publisher: Norwegian Biophysics Symposium

Morphological imaging of 3D cultured kidney mesangial cells using gradient light interference microscopy (opens in new window)

Author(s): Ankit Butola, Biswajoy Ghosh, Jaena Park, Minsung Kwon, Alejandro De la Cadena, Sudipta Mukherjee, Rohit Bhargava, Stephen A Boppart, Krishna Agarwal
Published in: Optica Digital Holography and Three-Dimensional Imaging 2024 (DH), 2024, Page(s) M2B.4
Publisher: Optica Publishing Group
DOI: 10.1364/dh.2024.m2b.4

Multiple signal classification algorithm – a versatile super-resolution and contrast enhancement approach

Author(s): Krishna Agarwal
Published in: Focus on Microscopy, 2025, 2025
Publisher: Focus on Microscopy

Adapation of subspace based optimization method for dark field microscopy data

Author(s): Y. Qin and K. Agarwal
Published in: IEEE International Symposium on Antennas and Propagation and ITNC-USNC-URSI Radio Science Meeting, 2024
Publisher: IEEE

Shape based forward solver for multi-nested body in label-free microscopy

Author(s): Yi Huang, Yingying Qin, Krishna Agarwal
Published in: TNNN Conference, 2025
Publisher: TNNN

MUSICAL – a versatile super-resolution microscopy solution for gentle imaging of physical characteristics of biological samples

Author(s): Sebastian Acuña, Krishna Agarwal
Published in: 4th International Conference On Optics, Photonics, And Lasers, 2023
Publisher: OPL

Forward modeling of mesoscopic imaging with radiative transfer equation”, Focus on Microscopy

Author(s): Yingying Qin, Yu Zhong, Krishna Agarwal
Published in: Focus on Microscopy, 2025, 2025
Publisher: Focus on Microscopy

Multiscale resolution in structured illumination microscopy

Author(s): Ankit Butola, Sebastian Acuña, Daniel Henry Hansen, and Krishna Agarwal
Published in: Advances in Microscopic Imaging IV, 2023
Publisher: Advances in Microscopic Imaging

Phase Correlation Spectroscopy: Microparticles Diffusion Coefficient Determination (opens in new window)

Author(s): Sunil Bhatt, Himanshu Joshi, Ankit Butola, Krishna Agarwal, Dalip Singh Mehta
Published in: Optica Digital Holography and Three-Dimensional Imaging 2024 (DH), 2024, Page(s) W4A.8
Publisher: Optica Publishing Group
DOI: 10.1364/dh.2024.w4a.8

Learning Nanoscale Motion Patterns of Vesicles in Living Cells (opens in new window)

Author(s): Arif Ahmed Sekh, Ida Sundvor Opstad, Asa Birna Birgisdottir, Truls Myrmel, Balpreet Singh Ahluwalia, Krishna Agarwal, Dilip K. Prasad
Published in: 2020 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), 2020, Page(s) 14011-14020, ISBN 978-1-7281-7168-5
Publisher: IEEE
DOI: 10.1109/cvpr42600.2020.01403

Full-wave multiple-scattering forward modeling for conventional label-free microscope

Author(s): Y. Qin, A. Butola, K. Agarwal
Published in: Focus on Microscopy, 2023
Publisher: Focus on Microscopy

Multimodal nanoscopy and phase microscopy for 3D morphological imaging of liver sinusoidal endothelial cells

Author(s): A. Butola, D.A. Coucheron, P. McCourt, K. Agarwal, B.S. Ahluwalia
Published in: Focus on Microscopy, 2023
Publisher: Focus on Microscopy

Image Inpainting With Hypergraphs for Resolution Improvement in Scanning Acoustic Microscopy

Author(s): A. Somani, Pragyan Banerjee, Manu Rastogi, Krishna Agarwal, Dilip K. Prasad, and Anowarul Habib
Published in: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2023
Publisher: IEEE

MUSICAL: a family of computational techniques for fluorescence nanoscopy

Author(s): S.A. Acuña, I. S. Opstad, L.E. Villegas-Hernández, B.S. Ahluwalia, K. Agarwal
Published in: Focus on Microscopy, 2023
Publisher: Focus on Microscopy

Motion trace analysis based on label-free imaging andMUSICAL

Author(s): Sunil Bhatt, Ankit Butola, Dalip Singh Mehta, and Krishna Agarwal
Published in: Norwegian Electro-Optics Meeting, 2022
Publisher: Optics Group of the Norwegian Physical Society

Adaptation and performance of well known non-linear inverse solvers in optical microscopy

Author(s): Yingying Qin, Ankit Butola, Krishna Agarwal
Published in: IEEE International Symposium on Antennas and Propagation and ITNC-USNC-URSI Radio Science Meeting, 2024
Publisher: IEEE

Quantitative phase imaging and on-chip nanoscopy for 3D imaging of liver sinusoidal endothelial cells

Author(s): Ankit Butola, David A. Coucheron, Karolina Szafranska, Azeem Ahmad, Hong Mao, Jean-Claude Tinguely, Peter McCourt, Paramasivam Senthilkumaran, Dalip Singh Mehta, Krishna Agarwal, Balpreet Singh Ahluwalia
Published in: Digital Holography and 3-D Imaging 2022, 2022, ISBN 978-1-957171-12-8
Publisher: Optica

MUSICAL – a versatile computational nanoscopy approach

Author(s): Sebastian Acuña and Krishna Agarwal
Published in: European Summit On Laser Optics & Photonics Technology, 2023
Publisher: ELOPS

Quantitative phase imaging and machine learning for spermatozoa analysis (opens in new window)

Author(s): Ankit Butola, Sigurd Hellberg, Mona Nystad, Krishna Agarwal
Published in: Optica Imaging Congress 2024 (3D, AOMS, COSI, ISA, pcAOP), 2024, Page(s) JM4A.6
Publisher: Optica Publishing Group
DOI: 10.1364/3d.2024.jm4a.6

Physics-guided loss functions improve the performance of deep learning in inverse scattering problems

Author(s): Zicheng Liu, Krishna Agarwal
Published in: Photonics and Electromagnetics Research Symposium, 2024
Publisher: PIERS

3D refractive index reconstruction from phaseless coherent label-free microscope

Author(s): Yingying Qin, Ankit Butola, Yu Zhong, Krishna Agarwal
Published in: Focus on Microscopy, 2025, 2025
Publisher: Focus on Microscopy

Nanoscale motion tracing and correlation analysis between cell parameters in human spermatozoa (opens in new window)

Author(s): Sunil Bhatt, Ankit Butola, Anuj Saxena, Krishna Agarwal, Dalip Singh Mehta
Published in: Quantitative Phase Imaging XI, 2025, Page(s) 85
Publisher: SPIE
DOI: 10.1117/12.3050760

Intellectual Property Rights

Other (1)
Transmission-SIM

Application/Publication number: PCT/GB 2020/052456
Date: 2020-10-05
Applicant(s): UNIVERSITETET I TROMSOE - NORGES ARKTISKE UNIVERSITET

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Last update: 1 September 2025

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