Dynamic adaptive microscopy for label-free multi-parametric imaging in biology and medicine

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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 .

Deliverables

Optimization algorithms

Development of initial optimization and transmission matrix calculation algorithms. New concepts to account for refractive index variations with adaptive meshing, Levy statistics and Monte Carlo modelling of light propagation in complex media

Phase retrieval

Development of 3D autocorrelation phase and polarization retrieval algorithms exploiting coherent multiply scattered light in optical, optoacoustic, non-linear and Raman methods

Non-diffracting illumination

Non-diffracting beam formation strategies with appropriate spatial filtering (reconfigurable photonic, biological and biomimetic structures) and coherent structured and speckle illumination

Adaptive module

Combine ultrafast wavefront shaping adaptive optomechatronics technologies (build in WP3 and WP4) in one microscopy enabled module

SRS full integration

Build coherent stimulated Raman Scattering (SRS) ability for fast identification of molecular fingerprints (identified in Task 6.2)

Integrated system

Integrate the different technologies and methods in a single prototype microscopy system, optimizing its operational characteristics in terms of sensitivity and specificity and identify safety appropriateness for animal and human use

Molecular/Proteomic fingerprints

Steer morphological & molecular fingerprinting (Raman) towards clinically related targets / questions by adapted fast Stimulated Raman Scattering (SRS) against the identified proteomic biomarkers (built in Task 5.3)

Raman analysis

Using a conventional Raman imaging system to analyse spectral signatures in relation to proteomic knowledge and identify molecules/proteins of clinical interest

In vivo assessment

Assess in vivo imaging ability of system in animals (rat, rabbit and pig; years 3, 4) and clinical relevance of new techniques and markers derived thereof in comparison with established clinical procedures and diagnostic markers

Dissemination and Exploitation final plan

Implemented actions of our dissemination, exploitation plan, and IPR management. Our industrial partners Rayfos and Imagine Optic and the DC have been appointed for coordinating this highly important task

Dissemination and Exploitation plan

Design of our dissemination, exploitation plan and IPR management. Our industrial partners Rayfos and Imagine Optic and the DC have been appointed for coordinating this highly important task

Dissemination and Exploitation interim plan

Implemented actions of our dissemination exploitation plan and IPR management Our industrial partners Rayfos and Imagine Optic and the DC have been appointed for coordinating this highly important task

Proof of concept

Proof of concept imaging and assessment of imaging prototype with freshly excised animal tissue samples retina cancer spheroids

Summer school

FORTH will organize a summer school on Biophotonics in Life Sciences, taking place on month 24. All involved parties will participate and leading scientists will be invited to teach the current state of the art as well as complimentary skills (IP management, entrepreneurship, proposal writing etc).

Website/Logo

Design of the project's logo and realization of the dedicated webpage with public sector and protected inranet for partners access only

Data management

Report on the data management plan of the consortium

Publications

Large field-of-view non-invasive imaging through scattering layers using fluctuating random illumination

Author(s): Lei Zhu, Fernando Soldevila, , Claudio Moretti, Alexandra d’Arco, Antoine Boniface, Xiaopeng Shao, Hilton B. de Aguiar & Sylvain Gigan
Published in: Nature Communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-29166-y

Spatially offset optical coherence tomography: Leveraging multiple scattering for high-contrast imaging at depth in turbid media

Author(s): GavrielleR. Untracht, MingzhouChen, PhilipWijesinghe, JosepMas, Harold T. Yura3, DominikMarti, PeterE. Andersen, KishanDholakia
Published in: Science Advances, 2023, ISSN 2375-2548
Publisher: American Association for the Advancement of Science
DOI: 10.1126/sciadv.adh5435

Hybrid confocal fluorescence and photoacoustic microscopy for the label-free investigation of melanin accumulation in fish scales

Author(s): George J. Tserevelakis, Michalis Pavlidis, Athanasios Samaras, Georgios D. Barmparis, Kostas G. Mavrakis, Ioannis Draganidis, Athanasios Oikonomou, Eleftheria Fanouraki, Giorgos P. Tsironis & Giannis Zacharakis
Published in: Scientific Reports, Issue Issue 12, 2022, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-022-11262-0

Stratigraphy of Fresco Paintings: A New Approach with Photoacoustic and SORS Imaging

Author(s): Francesca A. Pisu , Daniele Chiriu Evgenia Klironomou, Giannis Zacharakis and George J. Tserevelakis
Published in: Journal of Imaging, 2023, ISSN 2313-433X
Publisher: Francesca A. Pisu
DOI: 10.3390/jimaging9010016

Sidelobe suppressed Bessel beams for one-photon light-sheet microscopy

Author(s): Chetna Taneja, Jerin Geogy George, Stella Corsetti, Philip Wijesinghe, Graham D. Bruce, Maarten F. Zwart, Shanti Bhattacharya, Kishan Dholakia
Published in: Biomedical Optics Express, Issue 15, 2024, Page(s) 6183, ISSN 2156-7085
Publisher: The Optical Society
DOI: 10.1364/boe.538253

Complement Factor H Loss in RPE Cells Causes Retinal Degeneration in a Human RPE-Porcine Retinal Explant Co-Culture Model

Author(s): Angela Armento, Aparna Murali, Julia Marzi, Ana C Almansa-Garcia, Blanca Arango-Gonzalez, Ellen Kilger, Simon J Clark, Katja Schenke-Layland, Charmaine A Ramlogan-Steel, Jason C Steel, Marius Ueffing
Published in: Biomolecules, Issue 11, 2024, Page(s) 1621, ISSN 2218-273X
Publisher: MDPI
DOI: 10.3390/biom11111621

Online learning of the transmission matrix of dynamic scattering media

Author(s): Lorenzo Valzania, Sylvain Gigan
Published in: Optica, Issue 10, 2024, Page(s) 708, ISSN 2334-2536
Publisher: Optica
DOI: 10.1364/optica.479962

Optically generated droplet beams improve optoacoustic imaging of choroid thickness as an Alzheimer’s disease biomarker

Author(s): Kostas G. Mavrakis, Gerasimos Divaris, Maria Tampakaki, Saba N. Khan, Kishan Dholakia, Giannis Zacharakis
Published in: npj Nanophotonics, Issue 1, 2024, ISSN 2948-216X
Publisher: nature
DOI: 10.1038/s44310-024-00036-3

Roadmap on chaos-inspired imaging technologies (CI2-Tech)

Author(s): Joseph Rosen, Hilton B. de Aguiar, Vijayakumar Anand, YoonSeok Baek, Sylvain Gigan, Ryoichi Horisaki, Hervé Hugonnet, Saulius Juodkazis, KyeoReh Lee, Haowen Liang, Yikun Liu, Stephan Ludwig, Wolfgang Osten, YongKeun Park, Giancarlo Pedrini, Tushar Sarkar, Johannes Schindler, Alok Kumar Singh, Rakesh Kumar Singh, Guohai Situ, Mitsuo Takeda, Xiangsheng Xie, Wanqin Yang, Jianying Zhou
Published in: Applied Physics B, Issue 128, 2022, ISSN 0946-2171
Publisher: Springer Verlag
DOI: 10.1007/s00340-021-07729-z

A Cost-Efficient Multiwavelength LED-Based System for Quantitative Photoacoustic Measurements

Author(s): Michalis Orfanakis, George J. Tserevelakis, Giannis Zacharakis
Published in: Sensors, Issue 21/14, 2021, Page(s) 4888, ISSN 1424-8220
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/s21144888

A proton-inhibited DEG/ENaC ion channel maintains neuronal ionstasis and promotes neuronal survival under stress

Author(s): Dionysia Petratou, Martha Gjikolaj, Eva Kaulich, William Schafer, Nektarios Tavernarakis
Published in: iScience, 2023, ISSN 2589-0042
Publisher: Dionysia Petratou
DOI: 10.1016/j.isci.2023.107117

To focus-match or not to focus-match inverse spatially offset Raman spectroscopy: a question of light penetration

Author(s): Georgina E. Shillito, Lewis Mcmillan, Graham D. Bruce, and Kishan Dholakia
Published in: Optics Express, 2022, ISSN 1094-4087
Publisher: Optical Society of America
DOI: 10.1364/oe.451496

Hybrid Raman and Partial Wave Spectroscopy Microscope for the Characterization of Molecular and Structural Alterations in Tissue

Author(s): Elena Kriukova, Mikhail Mazurenka, Sabrina Marcazzan, Sarah Glasl, Michael Quante, Dieter Saur, Markus Tschurtschenthaler, Gerwin J. Puppels, Dimitris Gorpas, Vasilis Ntziachristos
Published in: Journal of Biophotonics, Issue 17, 2024, ISSN 1864-063X
Publisher: Wiley - VCH Verlag GmbH & CO. KGaA
DOI: 10.1002/jbio.202400330

MitoSNARE Assembly and Disassembly Factors Regulate Basal Autophagy and Aging in C. elegans

Author(s): Ilias Gkikas, Ioanna Daskalaki, Konstantinos Kounakis, Nektarios Tavernarakis, Eirini Lionaki
Published in: International Journal of Molecular Sciences, Issue 24, 2025, Page(s) 4230, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms24044230

Physics-based neural network for non-invasive control of coherent light in scattering media

Author(s): Alexandra d’Arco, Fei Xia, Antoine Boniface, Jonathan Dong, Sylvain Gigan
Published in: Optics Express, Issue 30, 2024, Page(s) 30845, ISSN 1094-4087
Publisher: Optical Society of America
DOI: 10.1364/oe.465702

High precision photoacoustic interferometer for the determination of the speed of sound in liquid media

Author(s): George J. Tserevelakis and Giannis Zacharakis
Published in: Optics Express, 2022
Publisher: George J. Tserevelakis
DOI: 10.1364/oe.455557

Agar Gel as a Non-Invasive Coupling Medium for Reflectance Photoacoustic (PA) Imaging: Experimental Results on Wall-Painting Mock-Ups

Author(s): Antonina Chaban , George J. Tserevelakis, Evgenia Klironomou, Giannis Zacharakis and Jana Striov
Published in: Journal of Imaging, 2022, ISSN 2313-433X
Publisher: Antonina Chaban
DOI: 10.3390/jimaging8090235

Full image reconstruction in frequency-domain photoacoustic microscopy by means of a low-cost I/Q demodulator

Author(s): George J. Tserevelakis, Kostas G. Mavrakis, Nikitas Kakakios, Giannis Zacharakis
Published in: Optics Letters, Issue 46/19, 2021, Page(s) 4718, ISSN 0146-9592
Publisher: Optical Society of America
DOI: 10.1364/ol.435146

Scattering correcting wavefront shaping for three-photon microscopy

Author(s): Bernhard Rauer, Hilton B. de Aguiar, Laurent Bourdieu, Sylvain Gigan
Published in: Optics Letters, Issue 47, 2024, Page(s) 6233, ISSN 0146-9592
Publisher: Optical Society of America
DOI: 10.1364/ol.468834

Label-free super-resolution stimulated Raman scattering imaging of biomedical specimens

Author(s): Julien Guilbert, Awoke Negash, Simon Labouesse, Sylvain Gigan, Anne Sentenac, Hilton B. de Aguiar
Published in: Advanced Imaging, Issue 1, 2024, Page(s) 011004, ISSN 2959-9539
Publisher: Researchng
DOI: 10.3788/ai.2024.10004

PML Differentially Regulates Growth and Invasion in Brain Cancer.

Author(s): Maria Tampakaki; Maria Tampakaki; Mariam-Eleni Oraiopoulou; Eleftheria Tzamali; Giorgos Tzedakis; Takis Makatounakis; Giannis Zacharakis; Joseph Papamatheakis; Joseph Papamatheakis; Vangelis Sakkalis
Published in: Issue 12, Issue 11, 2021, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms22126289

Neuronal atg1 Coordinates Autophagy Induction and Physiological Adaptations to Balance mTORC1 Signalling

Author(s): Athanasios Metaxakis Michail Pavlidis and Nektarios Tavernarakis
Published in: Cells, 2023, ISSN 2073-4409
Publisher: Athanasios Metaxakis
DOI: 10.3390/cells12162024

Non-Invasive Optoacoustic Imaging for In-Depth Cultural Heritage Diagnostics

Author(s): George J. Tserevelakis, Eleanna Pirgianaki, Kristalia Melessanaki, Giannis Zacharakis, Costas Fotakis
Published in: Photonics, Issue 11, 2024, Page(s) 902, ISSN 2304-6732
Publisher: Photonics
DOI: 10.3390/photonics11100902

Spermidine is essential for fasting-mediated autophagy and longevity

Author(s): Sebastian J. Hofer, Ioanna Daskalaki, Martina Bergmann, Jasna Friščić, Andreas Zimmermann, Melanie I. Mueller, Mahmoud Abdellatif, Raffaele Nicastro, Sarah Masser, Sylvère Durand, Alexander Nartey, Mara Waltenstorfer, Sarah Enzenhofer, Isabella Faimann, Verena Gschiel, Thomas Bajaj, Christine Niemeyer, Ilias Gkikas, Lukas Pein, Giulia Cerrato, Hui Pan, YongTian Liang, Jelena Tadic, Andrea Jerk
Published in: Nature Cell Biology, Issue 26, 2024, Page(s) 1571-1584, ISSN 1465-7392
Publisher: Nature Publishing Group
DOI: 10.1038/s41556-024-01468-x

Single-pixel transmission matrix recovery via two-photon fluorescence

Author(s): Shupeng Zhao, Bernhard Rauer, Lorenzo Valzania, Jonathan Dong, Ruifeng Liu, Fuli Li, Sylvain Gigan, Hilton B. de Aguiar
Published in: Science Advances, Issue 10, 2024, ISSN 2375-2548
Publisher: Science
DOI: 10.1126/sciadv.adi3442

Generation of Bessel-like beams with reduced sidelobes for enhanced light-sheet microscopy

Author(s): Jerin Geogy George, Kishan Dholakia, and Shanti Bhattacharya
Published in: Optics Continuum, 2023, ISSN 2770-0208
Publisher: Optica Publishing Group
DOI: 10.1364/optcon.493003

Non-invasive chemically selective energy delivery and focusing inside a scattering medium guided by Raman scattering

Author(s): Bingxin Tian, Bernhard Rauer, Antoine Boniface, Jun Han, Sylvain Gigan, Hilton B. de Aguiar
Published in: Optics Letters, Issue 47, 2024, Page(s) 2145, ISSN 0146-9592
Publisher: Optical Society of America
DOI: 10.1364/ol.456411

Local coordination of mRNA storage and degradation near mitochondria modulates C. elegans ageing

Author(s): Ioanna Daskalaki, Maria Markaki, Ilias Gkikas, Nektarios Tavernarakis
Published in: The EMBO Journal, 2023, ISSN 1460-2075
Publisher: Ioanna Daskalaki
DOI: 10.15252/embj.2022112446

Revealing Underdrawings in Wall Paintings of Complex Stratigraphy with a Novel Reflectance Photoacoustic Imaging Prototype

Author(s): Antonina Chaban, George J. Tserevelakis, Evgenia Klironomou, Raffaella Fontana, Giannis Zacharakis, Jana Striova
Published in: Journal of Imaging, Issue 7, 2025, Page(s) 250, ISSN 2313-433X
Publisher: MDPI
DOI: 10.3390/jimaging7120250

Phase conjugation with spatially incoherent light in complex media

Author(s): YoonSeok Baek, Hilton B. de Aguiar & Sylvain Gigan
Published in: Nature Photonics, 2023, ISSN 1749-4885
Publisher: Nature Pub. Group
DOI: 10.1038/s41566-023-01254-5

Imaging Parhyale hawaiensis embryogenesis with frequency domain photoacoustic microscopy: A novel tool in developmental biology

Author(s): George J. Tserevelakis, Sofia Velentza, Ioannis Liaskas, Themis Archontidis, Anastasios Pavlopoulos, Giannis Zacharakis
Published in: Journal of Biophtonics, 2022, ISSN 1864-0648
Publisher: Wiley-VCH GmbH
DOI: 10.1002/jbio.202200202

Experimentally unsupervised deconvolution for light-sheet microscopy with propagation-invariant beams

Author(s): Philip Wijesinghe, Stella Corsetti, Darren J. X. Chow, Shuzo Sakata, Kylie R. Dunning and Kishan Dholakia
Published in: Light: Science & Applications, 2022, ISSN 2047-7538
Publisher: USTAN
DOI: 10.1038/s41377-022-00975-6

Meshless Monte Carlo radiation transfer method for curved geometries using signed distance functions

Author(s): Lewis McMillan, Graham D Bruce, Kishan Dholakia
Published in: Journal of Biomedical Optics, 2022, ISSN 1560-2281
Publisher: SPIE
DOI: 10.1117/1.jbo.27.8.083003

Roadmap on computational methods in optical imaging and holography [invited]

Author(s): Joseph Rosen, Simon Alford, Blake Allan, Vijayakumar Anand, Shlomi Arnon, Francis Gracy Arockiaraj, Jonathan Art, Bijie Bai, Ganesh M. Balasubramaniam, Tobias Birnbaum, Nandan S. Bisht, David Blinder, Liangcai Cao, Qian Chen, Ziyang Chen, Vishesh Dubey, Karen Egiazarian, Mert Ercan, Andrew Forbes, G. Gopakumar, Yunhui Gao, Sylvain Gigan, Paweł Gocłowski, Shivasubramanian Gopinath, Alon Greenbaum
Published in: Applied Physics B, Issue 130, 2024, ISSN 0946-2171
Publisher: Springer Verlag
DOI: 10.1007/s00340-024-08280-3

UVA Hyperspectral Light-Sheet Microscopy for Volumetric Metabolic Imaging: Application to Preimplantation Embryo Development

Author(s): Josephine Morizet, Darren Chow, Philip Wijesinghe, Erik Schartner, George Dwapanyin, Nicolas Dubost, Graham D. Bruce, Ellen Anckaert, Kylie Dunning, Kishan Dholakia
Published in: ACS Photonics, Issue 10, 2023, Page(s) 4177-4187, ISSN 2330-4022
Publisher: American Chemical Society
DOI: 10.1021/acsphotonics.3c00900

Assessing locomotory rate in response to food for the identification of neuronal and muscular defects in C. elegans

Author(s): Dionysia Petratou, Persefoni Fragkiadaki, Eirini Lionaki, Nektarios Tavernarakis
Published in: STAR Protocols, Issue 5, 2024, Page(s) 102801, ISSN 2666-1667
Publisher: ScienceDirect
DOI: 10.1016/j.xpro.2023.102801

Optoacoustic interferometric characterization system (OPTICS) for the evaluation of fuel quality through speed of sound measurements

Author(s): George J. Tserevelakis, Charalampos Astrinakis, Giannis Zacharakis
Published in: Ultrasonics, Issue 139, 2024, Page(s) 107291, ISSN 0041-624X
Publisher: Elsevier BV
DOI: 10.1016/j.ultras.2024.107291

Age-associated anatomical and physiological alterations in Caenorhabditis elegans

Author(s): Emmanuel Spanoudakis, Nektarios Tavernarakis
Published in: Mechanisms of Ageing and Development, 2023, ISSN 1872-6216
Publisher: Emmanuel Spanoudakis
DOI: 10.1016/j.mad.2023.111827

Remote control of autophagy and metabolism in the liver

Author(s): Ilias Gkikas, Ioanna Daskalaki, Konstantinos Kounakis, Nektarios Tavernarakis and Eirini Lionaki
Published in: Int. J. Mol. Sci., 2023, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms24044230

Bimodal optical and optoacoustic multiview microscope in the frequency-domain

Author(s): Mikis Mylonakis, George J. Tserevelakis, Georgios Vlachos, Eleftheria Fanouraki, Anastasios Pavlopoulos, Michalis Pavlidis, Giannis Zacharakis
Published in: Optics Letters, Issue 49, 2024, Page(s) 462, ISSN 0146-9592
Publisher: Optical Society of America
DOI: 10.1364/ol.510384

Hybrid Fluorescence and Frequency-Domain Photoacoustic Microscopy for Imaging Development of Parhyale hawaiensis Embryos

Author(s): George J. Tserevelakis, Emmanouela Tekonaki, Maria Kalogeridi, Ioannis Liaskas, Anastasios Pavlopoulos and Giannis Zacharakis
Published in: Photonics, 2023, ISSN 2304-6732
Publisher: George J. Tserevelakis,
DOI: 10.3390/photonics10030264

Revealing Hidden Features in Multilayered Artworks by Means of an Epi-Illumination Photoacoustic Imaging System

Author(s): George J. Tserevelakis, Antonina Chaban, Evgenia Klironomou, Kristalia Melessanaki, Jana Striova, Giannis Zacharakis
Published in: Journal of Imaging, Issue 7/9, 2021, Page(s) 183, ISSN 2313-433X
Publisher: George J. Tserevelakis, Antonina Chaban, Evgenia Klironomou, Kristalia Melessanaki, Jana Striova and Giannis Zacharakis
DOI: 10.3390/jimaging7090183

Hybrid Autofluorescence and Optoacoustic Microscopy for the Label-Free, Early and Rapid Detection of Pathogenic Infections in Vegetative Tissues

Author(s): George J. Tserevelakis, Andreas Theocharis, Stavroula Spyropoulou, Emmanouil Trantas, , Dimitrios Goumas, Filippos Ververidis and Giannis Zacharakis
Published in: Journal of Imaging, 2023, ISSN 2313-433X
Publisher: George J. Tserevelakis
DOI: 10.3390/jimaging9090176

Towards affordable biomedical imaging: Recent advances in low‐cost, high‐resolution optoacoustic microscopy

Author(s): Pavlos Kalitsounakis, Giannis Zacharakis, George J. Tserevelakis
Published in: Journal of Microscopy, 2024, ISSN 0022-2720
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/jmi.13378

Neurophotonics beyond the surface: unmasking the brain’s complexity exploiting optical scattering

Author(s): Fei Xia, Caio Vaz Rimoli, Walther Akemann, Cathie Ventalon, Laurent Bourdieu, Sylvain Gigan, Hilton B. de Aguiar
Published in: Neurophotonics, Issue 11, 2024, ISSN 2329-423X
Publisher: SPIE
DOI: 10.1117/1.nph.11.s1.s11510

Label-free super-resolution chemical imaging of biomedical specimens

Author(s): Julien Guilbert, Awoke Negash, Simon Labouesse, Sylvain Gigan, Anne Sentenac, Hilton B. de Aguiar
Published in: bioRxiv, 2021
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2021.05.14.444185

Intellectual Property Rights

AN ASSEMBLY OF OPTICAL ELEMENTS AND A METHOD FOR CONTROLLING LIGHT

Application/Publication number: 22 164624
Date: 2022-03-28
Applicant(s): IDRYMA TECHNOLOGIAS KAI EREVNAS

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