OrganVision: Technology for real-time visualizing and modelling of fundamental process in living organoids towards new insights into organ-specific health, disease, and recovery

Informazioni relative al progetto

OrganVision

ID dell’accordo di sovvenzione: 964800

DOI

10.3030/964800

Data della firma CE 27 Gennaio 2021

Data di avvio 1 Luglio 2021

Data di completamento 30 Giugno 2026

Finanziato da

• EXCELLENT SCIENCE - Future and Emerging Technologies (FET)

Costo totale

€ 3 694 188,75

Contributo UE

€ 3 694 188,75

Coordinato da

UNIVERSITETET I TROMSOE - NORGES ARKTISKE UNIVERSITET
Norway

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Risultati finali

Websites, patent fillings, videos etc. (1)

Website launch and logo

Website of OrganVision

Pubblicazioni

Conference proceedings (26)

Engineered heart tissue with a pharmacological off-switch as a tool to study theinfluence of cardiac work on cardiomyocyte maturation

Autori: Rajiven Srikantharajah, Tim Stüdemann, Christoph Manthey, Thomas Eschenhagen, Florian Weinberger
Pubblicato in: 2022, Pagina/e The submissions were abstract only and are open access.
Editore: ISHR World Congress

Transplanted iPSC-derived cardiomyocytes actively contribute to left ventricular function

Autori: Tim Stüdemann, Judith Rössinger, Christoph Manthey, Birgit Geertz, Rajiven Srikantharajah, Constantin von Bibra, Aya Shibamiya, Maria Köhne, Antonius Wiehler, J. Simon Wiegert, Thomas Eschenhagen, Florian Weinberger
Pubblicato in: 2022, Pagina/e The submissions were abstract only and are open access.
Editore: ISHR World Congress

THE TRANSLATIONAL PATH TO HEART REGENERATION: GENETIC APPROACHES

Autori: Florian Weinberger
Pubblicato in: 2022
Editore: CNIC Regeneration Symposium

Engineered heart tissue and optogenetics – a powerful and versatile combination

Autori: Karl-Felix Müller, Bangfen Pan, Julius Hansen, Julia Krause, Grit Höppner, Tim Stüdemann, Ingke Braren, Florian Weinberger, Arne Hansen, Christine E. Gee, Torsten Christ, Thomas Eschenhagen, Justus Stenzig
Pubblicato in: 2022, Pagina/e The submissions were abstract only and are open access.
Editore: ISHR World Congress

Blind reconstruction of challenging raw data outperforms commercial 3DSIM

Autori: I.S. Opstad, S. Acuña, S. Ströhl, F. Ströhl, B.S. Ahluwalia, K. Agarwal
Pubblicato in: 2023
Editore: Focus on Microscopy

Laser additive fabrication of tailored micro-optics

Autori: Marti Duocastella, Ernest Martí-Jerez, Salvatore Surdo
Pubblicato in: Proceedings Volume PC11989, Laser-based Micro- and Nanoprocessing XVI, 2022, Pagina/e The submissions are abstract only and open access. The videos of talks are on demand.
Editore: SPIE
DOI: 10.1117/12.2608835

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

Autori: Sebastian Acuña and Krishna Agarwal
Pubblicato in: 2023
Editore: 4th International Conference On Optics, Photonics, And Lasers (OPL-2023)

MUSI-tAF: autofluorescence-based super-resolution of collagen fibrils in fixed tissues for density estimation

Autori: B. Ghosh, S. Acuña, K. Agarwal
Pubblicato in: 2023
Editore: Focus on Microscopy

Contractile force of transplanted cardiomyocytes actively supports heartfunction after injury

Autori: Florian Weinberger
Pubblicato in: 2023
Editore: German Cardiac Society

A simple and flexible platform for optogenetic pacing in cardiac tissue engineering

Autori: Bangfen Pan, Julius Hansen, Tim Stüdemann, Florian Weinberger, Thomas Eschenhagen, Justus Stenzig
Pubblicato in: 2022, Pagina/e The submissions were abstract only and are open access.
Editore: ISHR World Congress

Toward faster and deeper optical microscopes by combining ultrasound with light

Autori: Marti Duocastella
Pubblicato in: 2023
Editore: Spanish and Portuguese Advanced Optical Meeting (SPAOM)

OrganVision - Nanoscopic window into the life of heart

Autori: Giulia De Poli, Krishna Agarwal
Pubblicato in: 2022
Editore: AI4future

Physics-guided Loss Functions Impact Performance of Deep-learning-based Inverse-scattering-problem Solver

Autori: K. Agarwal, Z. Liu, M. Roy, D. K. Prasad
Pubblicato in: 2023
Editore: Photonics and Electromagnetics Research Symposium (PIERS)

Acousto-Optic Light Engineering for High-Speed Microscopy

Autori: Martí Duocastella
Pubblicato in: 2022
Editore: Frontiers in Lasers and Applications

Human engineered heart tissue transplantation in a guinea pig chronic injury model

Autori: Florian Weinberger
Pubblicato in: 2023
Editore: International Society for Heart Research

MABNET: Master Assistant Buddy Network With Hybrid Learning for Image Retrieval

Autori: R. Agarwal, G. Das, S. Aggarwal, A. Horsch, D.K. Prasad
Pubblicato in: IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), 2023
Editore: IEEE
DOI: 10.1109/icassp49357.2023.10094987

Guided U-Net aided Efficient Image Data Storing with Shape Preservation

Autori: N. Banerjee, S. Malakar, D. K. Gupta, A. Horsch, D.K. Prasad
Pubblicato in: 2023
Editore: Asian Conference on Pattern Recognition (ACPR2023)

Project presentation

Autori: Matteo Bregonzio
Pubblicato in: 2022
Editore: GO BEYOND 2022

Reconstructing 3D shape from 3D ThunderSTORM Point Clouds

Autori: S. Jadhav, S. Majhi, A.S. Chowdhury, D.K. Prasad, K. Agarwal
Pubblicato in: 2023
Editore: Focus on Microscopy

Quantitative phase imaging of fast dynamic events using acousto-optics and pulsed illumination

Autori: Christos Alexandropoulos, Martí Duocastella
Pubblicato in: 2023
Editore: Focus on Microscopy

Gradient Light Interference Microscopy for labelfree detection of early changes in kidney cells embedded in a soft and stiff hydrogel matrix

Autori: B. Ghosh, K. A. Fenton, K. Agarwal
Pubblicato in: 2023
Editore: Focus on Microscopy

Stem-cell based heart repair – pharmacological perspective

Autori: Florian Weinberger
Pubblicato in: 2022, Pagina/e The submissions were abstract only and are open access.
Editore: ISHR World Congress

What is Good Enough Myocardial Repair, Recovery or Remission in Chronic HF? Basic Science Perspective

Autori: Florian Weinberger
Pubblicato in: 2022
Editore: U-Cars Symposium 2022

Finding an Appropriate Dose for Engineered Heart Tissue

Autori: Florian Weinberger
Pubblicato in: 2022
Editore: Cardiovascular Bioengineering Symposium

Kilohertz frequency encoded microscopy using acousto-optic deflectors

Autori: Andrea Marchese, Pietro Ricci, Peter Saggau, Martí Duocastella
Pubblicato in: 2023
Editore: Focus on Microscopy

Generation of human engineered heart tissue with a chemo- and optogenetic Off-On switch

Autori: Judith Rössinger, Tim Stüdemann, Aya Shibamiya, Torsten Christ, Thomas Eschenhagen, Florian Weinberger
Pubblicato in: 2022, Pagina/e The submissions were abstract only and are open access.
Editore: ISHR World Congress

Other (20)

Codeset: Modelling Irregularly Sampled Time Series Without Imputation

Autori: Rohit Agarwal
Pubblicato in: 2023
Editore: Github

MiShape: 3D Shape Modelling of Mitochondria in Microscopy

Autori: Abhinanda R. Punnakkal, Suyog S Jadhav, Alexander Horsch, Krishna Agarwal, Dilip K. Prasad
Pubblicato in: 2023
Editore: Arxiv

Replication Data for: Multiple signal classification as a blind reconstruction approach for three-dimensional structured illumination microscopy

Autori: Ida S. Opstad
Pubblicato in: 2023
Editore: DataverseNO

LysoTracker Deep Red exhibits photoconversion in multi-color structured illumination microscopy

Autori: Ida Sundvor Opstad, Kenneth Bowitz Larsen, Åsa Birna Birgisdottir, Krishna Agarwal
Pubblicato in: 2023
Editore: BiorXiv
DOI: 10.1101/2023.10.29.564502

Fluorescence microscopy videos of mitochondria in H9c2 cardiomyoblasts

Autori: Ida S. Opstad
Pubblicato in: 2023
Editore: DataverseNO

"""OrganVision: An ERC funded interdisciplinary collaboration project” invited talk at IMB conference"

Autori: A. B. Birgisdottir
Pubblicato in: 2022, Pagina/e The entire event was open for all. The program was broadcast on digital stream of university. temporary link to program is given.
Editore: IMB conference

Multifocus microscopy with optically sectioned axial superresolution

Autori: Ströhl, Florian; Hansen, Daniel Henry; Nager Grifo, Mireia; Birgisdottir, Åsa Birna
Pubblicato in: Numero 1, 2022
Editore: Arxiv
DOI: 10.48550/arxiv.2206.01257

"""Monitoring mitochondria degradation in cardiac cells"" invited talk at the NORHEART seminar ""Targeting mitochondria in cardiovascular disease"""

Autori: A. B. Birgisdottir
Pubblicato in: 2021
Editore: NORHEART seminar

Tool & Video Protocol: Tool on fluorescence microscopy images of fixed cardiomyoblasts

Autori: Abhinanda Punakkal et al.
Pubblicato in: 2023
Editore: JOVE

“Monitoring degradation of mitochondria in cardiac cells”, invited talk at Annual meeting of the Scandinavian Physiological Society

Autori: A. B. Birgisdottir
Pubblicato in: 2021, Pagina/e No abstracts or papers were submitted. Program is open access.
Editore: Scandinavian Physiological Society

Latent Graph Attention for Enhanced Spatial Context

Autori: Ayush Singh, Yash Bhambhu, Himanshu Buckchash, Deepak K. Gupta, Dilip K. Prasad
Pubblicato in: Arxiv, 2023
Editore: Arxiv
DOI: 10.48550/arxiv.2307.04149

Fluorescence microscopy videos of mitochondria and endosomes in H9c2 cardiomyoblasts

Autori: Ida S. Opstad
Pubblicato in: 2023
Editore: DataverseNO

pNNCLR: Stochastic Pseudo Neighborhoods for Contrastive Learning based Unsupervised Representation Learning Problems

Autori: Momojit Biswas, Himanshu Buckchash, Dilip K. Prasad
Pubblicato in: 2023
Editore: Arxiv
DOI: 10.48550/arxiv.2308.06983

Summer School Course Tutorial Codeset “Interpretable DL Playground”

Autori: Ayush Somani
Pubblicato in: 2023
Editore: Github

"""Marked increase in mitochondria degradation in engineered heart tissue during reperfusion"""

Autori: A. B. Birgisdottir and M.N. Grifo
Pubblicato in: 2023
Editore: Mimisbrunnr conference

MABNET: Master Assistant Buddy Network With Hybrid Learning for Image Retrieval

Autori: R. Agarwal
Pubblicato in: 2023
Editore: Github

Modelling Irregularly Sampled Time Series Without Imputation

Autori: Rohit Agarwal, Aman Sinha, Dilip K. Prasad, Marianne Clausel, Alexander Horsch, Mathieu Constant, Xavier Coubez
Pubblicato in: 2023
Editore: Arxiv
DOI: 10.48550/arxiv.2309.08698

Paper Code: Virtual Labeling of Mitochondria in Living Cells using Physics-guided Deep Learning

Autori: Ayush Somani
Pubblicato in: 2022
Editore: Github

Arctic LLM Workshop Hands-on Tutorial Session

Autori: Ayush Somani
Pubblicato in: 2023
Editore: Github

Dense Video Captioning: A Survey of Techniques, Datasets and Evaluation Protocols

Autori: Qasim, Iqra; Horsch, Alexander; Prasad, Dilip K.
Pubblicato in: Numero 1, 2023
Editore: Arxiv
DOI: 10.48550/arxiv.2311.02538

Peer reviewed articles (12)

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

Autori: Ida S. Opstad, Åsa B. Birgisdottir, Krishna Agarwal
Pubblicato in: Scientific Data, Numero vol. 11, 2024, Pagina/e Article 125, ISSN 2052-4463
Editore: Springer Nature
DOI: 10.1038/s41597-024-02970-5

Modulating cardiac physiology in engineered heart tissue with the bidirectional optogenetic tool BiPOLES

Autori: Barbora Schwarzová, Tim Stüdemann, Muhammed Sönmez, Judith Rössinger, Bangfen Pan, Thomas Eschenhagen, Justus Stenzig, J Simon Wiegert, Torsten Christ, Florian Weinberger
Pubblicato in: Pflugers Archive, European Journal of Physiology, 2023, ISSN 0031-6768
Editore: Springer Verlag
DOI: 10.1007/s00424-023-02869-x

Scan-less microscopy based on acousto-optic encoded illumination

Autori: Andrea Marchese , Pietro Ricci , Peter Saggau, Martí Duocastella
Pubblicato in: Nanophotonics, Numero Volume 13, Numero 1, 2024, Pagina/e 63-73, ISSN 2192-8614
Editore: Berlin de Gruyter
DOI: 10.1515/nanoph-2023-0616

TERMIS 2023 – European Chapter Manchester Central Conference Centre Manchester, UK March 28–31, 2023

Autori: Biswajoy Ghosh, Krishna Agarwal
Pubblicato in: Tissue Engineering Part A, 2023, ISSN 1937-3341
Editore: Mary Ann Liebert Inc.
DOI: 10.1089/ten.tea.2023.29043.abstracts

Multifocus microscopy with optical sectioning and high axial resolution

Autori: Florian Ströhl, Daniel Henry Hansen, Mireia Nager Grifo, Åsa Birna Birgisdottir
Pubblicato in: Optica, Numero Vol. 9, Numero 11, 2022, Pagina/e 1210-1218, ISSN 2334-2536
Editore: Optica Publishing Group
DOI: 10.1364/optica.468583

3D refractive index reconstruction from phaseless coherent optical microscopy data using multiple scattering-based inverse solvers - a study

Autori: Yingying Qin, Ankit Butola, Krishna Agarwal
Pubblicato in: Inverse Problems, Numero volume 40, no. 1, 2023, Pagina/e article 015003, ISSN 0266-5611
Editore: Institute of Physics Publishing
DOI: 10.1088/1361-6420/ad0c29

Abstract 14720: Marked Increase in Mitochondria Degradation in Engineered Heart Tissue During Reperfusion

Autori: Mireia Nager, Zambarlal Bhujabal, Kenneth B Bowitz Larsen, Trine B Kalstad, Truls Myrmel, Asa B Birgisdottir
Pubblicato in: Circulation, Numero 146, 2023, ISSN 0009-7322
Editore: Lippincott Williams & Wilkins Ltd.
DOI: 10.1161/circ.146.suppl_1.14720

Viewing life without labels under optical microscopes

Autori: Biswajoy Ghosh, Krishna Agarwal
Pubblicato in: Communication Biology, Numero vol. 6, 2023, Pagina/e article number 559, ISSN 2399-3642
Editore: Springer Nature
DOI: 10.1038/s42003-023-04934-8

Analyzing Mitochondrial Morphology Through Simulation Supervised Learning

Autori: Abhinanda Ranjit Punnakkal, Gustav Godtliebsen, Ayush Somani, Sebastian Andres Acuna Maldonado, Åsa Birna Birgisdottir, Dilip K. Prasad, Alexander Horsch, Krishna Agarwal
Pubblicato in: Journal of Visualized Experiments, 2024, ISSN 1940-087X
Editore: MYJoVE Corporation
DOI: 10.3791/64880-v

High-resolution visualization and assessment of basal and OXPHOS-induced mitophagy in H9c2 cardiomyoblasts

Autori: Gustav Godtliebsen, Kenneth Bowitz Larsen, Zambarlal Bhujabal, Ida S Opstad, Mireia Nager, Abhinanda R Punnakkal, Trine B Kalstad, Randi Olsen, Trine Lund, Dilip K Prasad, Krishna Agarwal, Truls Myrmel, Asa Birna Birgisdottir
Pubblicato in: Autophagy, Numero vol. 19, issue 10, 2023, Pagina/e 2769-2788, ISSN 1554-8627
Editore: Landes Bioscience
DOI: 10.1080/15548627.2023.2230837

Video-rate quantitative phase imaging with dynamic acousto-optic defocusing

Autori: Christos Alexandropoulos, Martí Duocastella
Pubblicato in: Optics and Lasers in Engineering, Numero Volume 169, October 2023, 2023, Pagina/e article 107692, ISSN 0143-8166
Editore: Elsevier BV
DOI: 10.1016/j.optlaseng.2023.107692

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

Autori: Ayush Somani, Arif Ahmed Sekh, Ida S. Opstad, Åsa Birna Birgisdottir, Truls Myrmel, Balpreet Singh Ahluwalia, Alexander Horsch, Krishna Agarwal, Dilip K. Prasad
Pubblicato in: Biomedical Optics Express, Numero Vol. 13, Numero 10, 2022, Pagina/e 5495-5516, ISSN 2156-7085
Editore: The Optical Society
DOI: 10.1364/boe.464177

Thesis and dissertations (6)

Reconstructing 3D Geometries of sub-cellular structures from SMLM clouds

Autori: S. Jadhav
Pubblicato in: 2023
Editore: UiT The Arctic University of Norway

Multiple Signal Classification Algorithm: A computational microscopy tool for fluorescence microscopy

Autori: Sebastián Andrés Acuña Maldonado
Pubblicato in: 2023
Editore: MUNIN, UiT

Presenting CODS (Cell Organelle Dynamic Simulation)

Autori: Aaron Celeste
Pubblicato in: 2023
Editore: UiT The Arctic University of Norway

Generative Adversarial Networks For Three-Dimensional Multi-Channel Virtual Fluorescent Staining

Autori: Lorenzo Venieri
Pubblicato in: 2024
Editore: Università di Bologna
DOI: 10.5281/zenodo.13382862

Study of mitochondrial transfer in hiPSC derived cardiomyocytes and engineered heart tissue

Autori: Kristiana Imsa
Pubblicato in: 2023
Editore: UiT The Arctic University of Norway

Encoded illumination for high-speed optical microscopy

Autori: Eva Maria Torres-Riera
Pubblicato in: 2023
Editore: Universitat Politecnica de Catalunya

Book chapters (1)

Auxiliary Network: Scalable and Agile Online Learning for Dynamic System with Inconsistently Available Inputs

Autori: Rohit Agarwal, Krishna Agarwal, Alexander Horsch, Dilip K. Prasad
Pubblicato in: Lecture Notes in Computer Science, Neural Information Processing, 2023, Pagina/e 549-561
Editore: Springer International Publishing
DOI: 10.1007/978-3-031-30105-6_46