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

Informations projet

3D-nanoMorph

N° de convention de subvention: 804233

DOI

10.3030/804233

Projet clôturé

Date de signature de la CE 25 Octobre 2018

Date de début 1 Juillet 2019

Date de fin 30 Juin 2025

Financé au titre de

• EXCELLENT SCIENCE - European Research Council (ERC)

Coût total

€ 1 499 999,00

Contribution de l’UE

€ 1 499 999,00

Coordonné par

UNIVERSITETET I TROMSOE - NORGES ARKTISKE UNIVERSITET
Norway

CORDIS fournit des liens vers les livrables publics et les publications des projets HORIZON.

Les liens vers les livrables et les publications des projets du 7e PC, ainsi que les liens vers certains types de résultats spécifiques tels que les jeux de données et les logiciels, sont récupérés dynamiquement sur OpenAIRE .

Publications

Other (5)

Guiding Artificial Intelligence Through Physics for Scientific Problems

Auteurs: Krishna Agarwal
Publié dans: IEEE SPS Webinar, 2024
Éditeur: IEEE

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

Auteurs: 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
Publié dans: Arxiv, Numéro 1, 2021
Éditeur: Arxiv
DOI: 10.48550/arxiv.2108.10575

Fluorescence fluctuations-based super-resolution microscopy techniques: an experimental comparative study

Auteurs: Opstad, Ida S.; Acu��a, Sebastian; Hernandez, Lu��s Enrique Villegas; Cauzzo, Jennifer; ��kalko-Basnet, Nata��a; Ahluwalia, Balpreet S.; Agarwal, Krishna
Publié dans: Arxiv, Numéro 1, 2021
Éditeur: Arxiv
DOI: 10.48550/arxiv.2008.09195

tAF-MUSICAL: Autofluorescence Super-resolution Microscopy for Molecular Histopathology of Matrix Proteins in Fibrotic Diseases

Auteurs: Biswajoy Ghosh, Jyotirmoy Chatterjee, Ranjan Paul, Pooja Lahiri, Mousumi Pal, Pabitra Mitra, Balpreet Singh Ahluwalia, Krishna Agarwal
Publié dans: 2024
Éditeur: Springer Science and Business Media LLC
DOI: 10.21203/rs.3.rs-101219/v1

High-resolution imaging in acoustic microscopy using deep learning

Auteurs: Pragyan Banerjee, Shivam Milind Akarte, Prakhar Kumar, Muhammad Shamsuzzaman, Krishna Agarwal , Ankit Butola,Dilip K. Prasad, Frank Melandsø, and Habib Anowarul
Publié dans: Researchsquare pre-print, 2022
Éditeur: Researchsquare
DOI: 10.21203/rs.3.rs-1669440/v1

Peer reviewed articles (24)

Soft thresholding schemes for multiple signal classification algorithm

Auteurs: Sebastian Acuña, Ida S. Opstad, Fred Godtliebsen, Balpreet Singh Ahluwalia, Krishna Agarwal
Publié dans: Optics Express, Numéro 28/23, 2020, Page(s) 34434, ISSN 1094-4087
Éditeur: Optical Society of America
DOI: 10.1364/oe.409363

Deriving high contrast fluorescence microscopy images through low contrast noisy image stacks

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

Physics-based machine learning for subcellular segmentation in living cells

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

Computational Comparison and Validation of Point Spread Functions for Optical Microscopes

Auteurs: Zicheng Liu, Yingying Qin, Jean-Claude Tinguely, Krishna Agarwal
Publié dans: IEEE Transactions on Computational Imaging, Numéro 11, 2025, Page(s) 170-178, ISSN 2333-9403
Éditeur: 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

Auteurs: 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
Publié dans: Proceedings of the National Academy of Sciences, Numéro 118/47, 2021, ISSN 1091-6490
Éditeur: National Academy of Science
DOI: 10.1073/pnas.2115323118

Taxonomy of hybridly polarized Stokes vortex beams

Auteurs: Arora, Gauri; Butola, Ankit; Rajput, Ruchi; Agarwal, Rohit; Agarwal, Krishna; Horsch, Alexander; Prasad, Dilip K; Senthilkumaran, Paramasivam
Publié dans: Optics Express, Numéro 1, 2024, ISSN 1094-4087
Éditeur: Optical Society of America
DOI: 10.48550/arxiv.2306.05974

Blind Super-Resolution Approach for Exploiting Illumination Variety in Optical-Lattice Illumination Microscopy

Auteurs: Krishnendu Samanta; Swagato Sarkar; Swagato Sarkar; Sebastian Acuña; Joby Joseph; Balpreet Singh Ahluwalia; Krishna Agarwal
Publié dans: ACS Photonics, Numéro 1, 2021, ISSN 2330-4022
Éditeur: American Chemical Society
DOI: 10.1021/acsphotonics.1c00503

Virtual labeling of mitochondria in living cells using correlative imaging and physics-guided deep learning

Auteurs: Ayush Somani; Arif Ahmed Sekh; Ida S. Opstad; Åsa Birna Birgisdottir; Truls Myrmel; Balpreet Singh Ahluwalia; Alexander Horsch; Krishna Agarwal; Dilip K. Prasad
Publié dans: Biomed Opt Express, Numéro 4, 2022, ISSN 2156-7085
Éditeur: 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

Auteurs: Nikhil Jayakumar, Øystein I. Helle, Krishna Agarwal, Balpreet Singh Ahluwalia
Publié dans: Optics Express, Numéro 28/24, 2020, Page(s) 35454, ISSN 1094-4087
Éditeur: Optical Society of America
DOI: 10.1364/oe.403804

Characterizing the consistency of motion of spermatozoa through nanoscale motion tracing

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

Physics-Guided Loss Functions Improve Deep Learning Performance in Inverse Scattering

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

Scalable-resolution structured illumination microscopy

Auteurs: Ankit Butola; Sebastian Acuna; Daniel Henry Hansen; Krishna Agarwal
Publié dans: Optics Express, Numéro 1, 2022, ISSN 1094-4087
Éditeur: Optical Society of America
DOI: 10.1364/oe.465303

Fluorescence microscopy and correlative brightfield videos of mitochondria and vesicles in H9c2 cardiomyoblasts

Auteurs: Ida S. Opstad, Åsa B. Birgisdottir, Krishna Agarwal
Publié dans: Scientific Data, Numéro 11, 2024, ISSN 2052-4463
Éditeur: Springer Science and Business Media LLC
DOI: 10.1038/s41597-024-02970-5

Object detection neural network improves Fourier ptychography reconstruction

Auteurs: Florian Ströhl, Suyog Jadhav, Balpreet S. Ahluwalia, Krishna Agarwal, Dilip K. Prasad
Publié dans: Optics Express, Numéro 28/25, 2020, Page(s) 37199, ISSN 1094-4087
Éditeur: Optical Society of America
DOI: 10.1364/oe.409679

MusiJ: an ImageJ plugin for video nanoscopy

Auteurs: Sebastian Acuña, Florian Ströhl, Ida S. Opstad, Balpreet S. Ahluwalia, Krishna Agarwal
Publié dans: Biomedical Optics Express, Numéro 11/5, 2020, Page(s) 2548, ISSN 2156-7085
Éditeur: The Optical Society
DOI: 10.1364/boe.382735

Single-shot multispectral quantitative phase imaging of biological samples using deep learning

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

Artefact removal in ground truth deficient fluctuations-based nanoscopy images using deep learning

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

PyQPI: Open source python framework for the reconstruction of off-axis quantitative phase imaging

Auteurs: Ankit Butola, Sigurd Hellberg, Hong Mao, Krishna Agarwal
Publié dans: Optics & Laser Technology, Numéro 181, 2024, Page(s) 111606, ISSN 0030-3992
Éditeur: Elsevier BV
DOI: 10.1016/j.optlastec.2024.111606

Analyzing Mitochondrial Morphology Through Simulation Supervised Learning

Auteurs: Krishna Agarwal; Alexander Horsch; Dilip K. Prasad; Åsa Birna Birgisdottir; Sebastian Andres Acuna Maldonado; Ayush Somani; Gustav Godtliebsen; Abhinanda Ranjit Punnakkal
Publié dans: Optics Express, Numéro 1, 2022, ISSN 1094-4087
Éditeur: Optical Society of America
DOI: 10.3791/64880-v

Molecular histopathology of matrix proteins through autofluorescence super-resolution microscopy

Auteurs: Biswajoy Ghosh, Jyotirmoy Chatterjee, Ranjan Rashmi Paul, Sebastian Acuña, Pooja Lahiri, Mousumi Pal, Pabitra Mitra, Krishna Agarwal
Publié dans: Scientific Reports, Numéro 14, 2024, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-024-61178-0

Silicon substrate significantly alters dipole-dipole resolution in coherent microscope

Auteurs: Zicheng Liu, Krishna Agarwal
Publié dans: Optics Express, Numéro 28/26, 2020, Page(s) 39713, ISSN 1094-4087
Éditeur: Optical Society of America
DOI: 10.1364/oe.409629

Multi-moded high-index contrast optical waveguide for super-contrast high-resolution label-free microscopy

Auteurs: 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
Publié dans: Nanophotonics, Numéro 2, 2022, ISSN 2330-4022
Éditeur: American Chemical Society
DOI: 10.1515/nanoph-2022-0100

Single-shot multispectral quantitative phase imaging using deep neural network

Auteurs: Bhatt, Sunil; Butola, Ankit; Kumar, Anand; Thapa, Pramila; Joshi, Akshay; Singh, Neetu; Agarwal, Krishna; Mehta, Dalip Singh
Publié dans: Applied Optics, Numéro 1, 2023, ISSN 1559-128X
Éditeur: 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

Auteurs: Yingying Qin; Ankit Butola; Krishna Agarwal
Publié dans: Inverse Problems, Numéro 1, 2024, ISSN 0266-5611
Éditeur: 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

Auteurs: Yi Huang, Yingying Qin, Krishna Agarwal
Publié dans: Focus on Microscopy, 2025, 2025
Éditeur: Focus on Microscopy

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

Auteurs: Biswajoy Ghosh, Krishna Agarwal
Publié dans: Focus on Microscopy, 2025, 2025
Éditeur: Focus on Microscopy

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

Auteurs: Sunil Bhatt, Ankit Butola, Sebastian Acuña, Daniel Henry Hansen, Jean-Claude Tinguely, Dalip Singh Mehta, Balpreet Singh Ahluwalia, and Krishna Agarwal
Publié dans: Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XXI, 2023
Éditeur: SPIE

Blind reconstruction of challenging raw data outperforms commercial 3DSIM

Auteurs: I.S. Opstad, S. Acuña, S. Ströhl, F. Ströhl, B.S. Ahluwalia, K. Agarwal
Publié dans: Focus on Microscopy, 2023
Éditeur: Focus on Microscopy

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

Auteurs: Yingying Qin, Ankit Butola, Krishna Agarwal
Publié dans: Photonics and Electromagnetics Research Symposium, 2024
Éditeur: PIERS

Multiscale resolution in Structured illumination microscopy

Auteurs: A. Butola, S. Acuna, D.H. Hansen, K. Agarwal
Publié dans: Focus on Microscopy, 2023
Éditeur: Focus on Microscopy

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

Auteurs: Yingying Qin, Yu Zhong and Krishna Agarwal
Publié dans: International Conference on Electromagnetics in Advanced Applications, Numéro ICEAA – IEEE APWC 2025, 2026
Éditeur: IEEE

Enhancing and exploiting multiple scattering in label-free microscopy

Auteurs: Krishna Agarwal
Publié dans: Norwegian Biophysics Symposium, 2024
Éditeur: Norwegian Biophysics Symposium

Morphological imaging of 3D cultured kidney mesangial cells using gradient light interference microscopy

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

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

Auteurs: Krishna Agarwal
Publié dans: Focus on Microscopy, 2025, 2025
Éditeur: Focus on Microscopy

Adapation of subspace based optimization method for dark field microscopy data

Auteurs: Y. Qin and K. Agarwal
Publié dans: IEEE International Symposium on Antennas and Propagation and ITNC-USNC-URSI Radio Science Meeting, 2024
Éditeur: IEEE

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

Auteurs: Yi Huang, Yingying Qin, Krishna Agarwal
Publié dans: TNNN Conference, 2025
Éditeur: TNNN

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

Auteurs: Sebastian Acuña, Krishna Agarwal
Publié dans: 4th International Conference On Optics, Photonics, And Lasers, 2023
Éditeur: OPL

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

Auteurs: Yingying Qin, Yu Zhong, Krishna Agarwal
Publié dans: Focus on Microscopy, 2025, 2025
Éditeur: Focus on Microscopy

Multiscale resolution in structured illumination microscopy

Auteurs: Ankit Butola, Sebastian Acuña, Daniel Henry Hansen, and Krishna Agarwal
Publié dans: Advances in Microscopic Imaging IV, 2023
Éditeur: Advances in Microscopic Imaging

Phase Correlation Spectroscopy: Microparticles Diffusion Coefficient Determination

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

Learning Nanoscale Motion Patterns of Vesicles in Living Cells

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

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

Auteurs: Y. Qin, A. Butola, K. Agarwal
Publié dans: Focus on Microscopy, 2023
Éditeur: Focus on Microscopy

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

Auteurs: A. Butola, D.A. Coucheron, P. McCourt, K. Agarwal, B.S. Ahluwalia
Publié dans: Focus on Microscopy, 2023
Éditeur: Focus on Microscopy

Image Inpainting With Hypergraphs for Resolution Improvement in Scanning Acoustic Microscopy

Auteurs: A. Somani, Pragyan Banerjee, Manu Rastogi, Krishna Agarwal, Dilip K. Prasad, and Anowarul Habib
Publié dans: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2023
Éditeur: IEEE

MUSICAL: a family of computational techniques for fluorescence nanoscopy

Auteurs: S.A. Acuña, I. S. Opstad, L.E. Villegas-Hernández, B.S. Ahluwalia, K. Agarwal
Publié dans: Focus on Microscopy, 2023
Éditeur: Focus on Microscopy

Motion trace analysis based on label-free imaging andMUSICAL

Auteurs: Sunil Bhatt, Ankit Butola, Dalip Singh Mehta, and Krishna Agarwal
Publié dans: Norwegian Electro-Optics Meeting, 2022
Éditeur: Optics Group of the Norwegian Physical Society

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

Auteurs: Yingying Qin, Ankit Butola, Krishna Agarwal
Publié dans: IEEE International Symposium on Antennas and Propagation and ITNC-USNC-URSI Radio Science Meeting, 2024
Éditeur: IEEE

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

Auteurs: 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
Publié dans: Digital Holography and 3-D Imaging 2022, 2022, ISBN 978-1-957171-12-8
Éditeur: Optica

MUSICAL – a versatile computational nanoscopy approach

Auteurs: Sebastian Acuña and Krishna Agarwal
Publié dans: European Summit On Laser Optics & Photonics Technology, 2023
Éditeur: ELOPS

Quantitative phase imaging and machine learning for spermatozoa analysis

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

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

Auteurs: Zicheng Liu, Krishna Agarwal
Publié dans: Photonics and Electromagnetics Research Symposium, 2024
Éditeur: PIERS

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

Auteurs: Yingying Qin, Ankit Butola, Yu Zhong, Krishna Agarwal
Publié dans: Focus on Microscopy, 2025, 2025
Éditeur: Focus on Microscopy

Nanoscale motion tracing and correlation analysis between cell parameters in human spermatozoa

Auteurs: Sunil Bhatt, Ankit Butola, Anuj Saxena, Krishna Agarwal, Dalip Singh Mehta
Publié dans: Quantitative Phase Imaging XI, 2025, Page(s) 85
Éditeur: SPIE
DOI: 10.1117/12.3050760

Droits de propriété intellectuelle

Other (1)

Transmission-SIM

Numéro de demande/publication: PCT/GB 2020/052456
Date: 2020-10-05
Demandeur(s): UNIVERSITETET I TROMSOE - NORGES ARKTISKE UNIVERSITET