Imaging infections: integrated, multiscale visualization of infections and host response

Project Information

IMAGE-IN

Grant agreement ID: 861122

DOI

10.3030/861122

Project closed

EC signature date 5 July 2019

Start date 1 January 2020

End date 30 June 2024

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 1 233 805,68

EU contribution

€ 1 233 805,68

Coordinated by

LEIBNIZ-INSTITUT FUER PHOTONISCHE TECHNOLOGIEN E.V.
Germany

CORDIS provides links to public deliverables and publications of HORIZON projects.

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

Documents, reports (6)

PhD awarded

PhD titles have been awarded to the ESRs.

Summary of scientific publications and other modes of dissemination and outreach

Summary of scientific publications and other modes of dissemination and outreach and published online.

Potential inputs for policy feedback
Performance assessment of the different imaging approaches at different scales

Performance assessment of the different imaging approaches at different scales will be performed and prepared as a report deliverable.

PhD thesis submitted

ESR have their PhD theses submitted.

List of 5 selected candidates

5 ESR candidates have been selected A list is prepared as a report

Other (3)

Supervisory Board of the network

Supervisory Board of the network establised

Data Visualization Framework

This deliverable will provide the development of tools for features visual representation and a system for co-registered structural, functional and molecular imaging with millimeter-scale imaging depth.

Content Discovery and Retrieval Platform

In this task, we expect to provide an important contribution in the field of information retrieval, as also strengthen the collaboration between partners (BMD and Leibniz-IPHT), which have a thorough knowledge of cross-modality data analysis and data fusion. The main output will be an extensible architecture for multimodal information retrieval, supporting new algorithms without major changes to the software, thus providing a multimodal layer of abstraction over the large domain of existing retrieval algorithms, such as feature extractors and model representations. Automated content discovery mechanism will be considered beneficial: the automatic detection of complex patterns in visual content introduces new concepts in medical image retrieval. In light of these ideas, it will be studied the subject of automated object recognition in spectroscopic data and medical images, followed by the design of an architecture for information enrichment of integrated archives through automatic extraction and indexing of visual information.

Websites, patent fillings, videos etc. (2)

IMAGE-IN positions are announced in the public channels

IMAGEIN positions are announced in the public channels

Website online

Project website has been created and is online

Publications

Peer reviewed articles (10)

DICOMization of Proprietary Files Obtained from Confocal, Whole-Slide, and FIB-SEM Microscope Scanners

Author(s): Yubraj Gupta, Carlos Costa, Eduardo Pinho, Luís Bastião Silva
Published in: Sensors, Issue 22, 2024, Page(s) 2322, ISSN 1424-8220
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/s22062322

A Data Augmentation Methodology to Reduce the Class Imbalance in Histopathology Images

Author(s): Rodrigo Escobar Díaz Guerrero, Lina Carvalho, Thomas Bocklitz, Juergen Popp, José Luis Oliveira
Published in: Journal of Imaging Informatics in Medicine, Issue 37, 2024, Page(s) 1767-1782, ISSN 2948-2933
Publisher: Journal of Digital Imaging. Inform. med.
DOI: 10.1007/s10278-024-01018-9

Software tools and platforms in Digital Pathology: a review for clinicians and computer scientists

Author(s): Rodrigo Escobar Díaz Guerrero, Lina Carvalho, Thomas Bocklitz, Juergen Popp, José Luis Oliveira
Published in: Journal of Pathology Informatics, Issue 13, 2024, Page(s) 100103, ISSN 2153-3539
Publisher: Journal of Pathology Informatics
DOI: 10.1016/j.jpi.2022.100103

Insights into S. aureus-Induced Bone Deformation in a Mouse Model of Chronic Osteomyelitis Using Fluorescence and Raman Imaging

Author(s): Shibarjun Mandal, Astrid Tannert, Christina Ebert, Rustam R. Guliev, Yvonne Ozegowski, Lina Carvalho, Britt Wildemann, Simone Eiserloh, Sina M. Coldewey, Bettina Löffler, Luís Bastião Silva, Verena Hoerr, Lorena Tuchscherr, Ute Neugebauer
Published in: International Journal of Molecular Sciences, Issue 24, 2023, Page(s) 9762, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms24119762

MMIR: an open-source software for the registration of multimodal histological images

Author(s): Rodrigo Escobar Díaz Guerrero, José Luis Oliveira, Juergen Popp, Thomas Bocklitz
Published in: BMC Medical Informatics and Decision Making, Issue 24, 2024, ISSN 1472-6947
Publisher: BioMed Central
DOI: 10.1186/s12911-024-02424-3

Correlation of crystal violet biofilm test results of Staphylococcus aureus clinical isolates with Raman spectroscopic read‐out

Author(s): Christina Ebert; Lorena Tuchscherr; Nancy Unger; Christine Pöllath; Frederike Gladigau; Jürgen Popp; Bettina Löffler; Ute Neugebauer
Published in: Journal of Raman Spectroscopy, Issue 1, 2021, Page(s) 2660-2670, ISSN 1097-4555
Publisher: WILEY
DOI: 10.1002/jrs.6237

IMAGE-IN: Interactive web-based multidimensional 3D visualizer for multi-modal microscopy images

Author(s): Yubraj Gupta, Carlos Costa, Eduardo Pinho, Luís A. Bastião Silva, Rainer Heintzmann
Published in: PLOS ONE, Issue 17, 2023, Page(s) e0279825, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0279825

High-throughput Raman spectroscopy allows <i>ex vivo</i> characterization of murine small intestinal intra-epithelial lymphocytes (IEL)

Author(s): Rustam R. Guliev, Tina Vogler, Natalie Arend, Simone Eiserloh, Alexander Wiede, Timo Kunert, Martin Dinkel, Jürgen Popp, Iwan W. Schie, Kai Hildner, Ute Neugebauer
Published in: The Analyst, Issue 148, 2024, Page(s) 1978-1990, ISSN 0003-2654
Publisher: Royal Society of Chemistry
DOI: 10.1039/d3an00074e

Label-Free Characterization of Macrophage Polarization Using Raman Spectroscopy

Author(s): Max Naumann, Natalie Arend, Rustam R. Guliev, Christian Kretzer, Ignacio Rubio, Oliver Werz, Ute Neugebauer
Published in: International Journal of Molecular Sciences, Issue 24, 2024, Page(s) 824, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms24010824

Findaureus: An open-source application for locating Staphylococcus aureus in fluorescence-labelled infected bone tissue slices

Author(s): Shibarjun Mandal, Astrid Tannert, Bettina Löffler, Ute Neugebauer, Luís Bastião Silva
Published in: PLOS ONE, Issue 19, 2024, Page(s) e0296854, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0296854

Conference proceedings (7)

A Multimodal Image Registration System for Histology Images

Author(s): Rodrigo Escobar Díaz Guerrero, Yubraj Gupta, Thomas Bocklitz, José Luis Oliveira
Published in: 2023 IEEE 36th International Symposium on Computer-Based Medical Systems (CBMS), 2024, Page(s) 17-22, ISSN 2372-9198
Publisher: IEEE
DOI: 10.1109/cbms58004.2023.00185

Improving the Visualization and Dicomization process for the Stacked Whole Slide Imaging

Author(s): Yubraj Gupta, Carlos Costa, Eduardo Pinho and Luis A. Bastiao Silva
Published in: IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2021), 2021
Publisher: IEEE
DOI: 10.1109/bibm52615.2021.9669349

Interactive Web-based 3D Viewer for Multidimensional Microscope Imaging Modalities

Author(s): Yubraj Gupta, Rodrigo E. D. Guerrero, Carlos Costa, Rui Jesus, Eduardo Pinho, Luis A. Bastiao Silva
Published in: 2022 26th International Conference Information Visualisation (IV), Issue 11, 2024, Page(s) 379-384, ISBN 978-1-6654-9007-8
Publisher: IEEE
DOI: 10.1109/iv56949.2022.00069

A DICOM Standard Pipeline for Microscope Imaging Modalities

Author(s): Yubraj Gupta, Carlos Costa, Eduardo Pinho and Luis A. Bastiao Silva
Published in: 26th IEEE Symposium on Computers and Communications (ISCC 2021), 2021
Publisher: IEEE
DOI: 10.1109/iscc53001.2021.9631529

Improvements in lymphocytes detection using deep learning with a preprocessing stage

Author(s): Rodrigo Escobar Díaz Guerrero, José Luís Oliveira
Published in: IEEE 34th International Symposium on Computer-Based Medical Systems (CBMS 2021), 2021
Publisher: IEEE
DOI: 10.1109/cbms52027.2021.00068

COMPARATIVE ANALYSIS OF H&E AND FLUORESCENCE IMAGES OF BONES IN EXPERIMENTAL HEMATOGENOUS OSTEOMYELITIS MOUSE MODELS

Author(s): Shibarjun Mandal, Astrid Tannert, Verena Hoerr, Carol Geppert, Lina Carvalho, Bettina Löffler, Luís Bastião Silva, Ute Neugebauer
Published in: Focus on Microscopy 2021, Issue March 2021, 2021
Publisher: Focus on Microscopy 2021
DOI: 10.13140/rg.2.2.11590.60482

Dicomization of LSM fluorescence composite microscope image with its bioimaging information

Author(s): Yubraj Gupta, Carlos Costa, Eduardo Pinho and Luis A. Bastiao Silva
Published in: IEEE 34th International Symposium on Computer-Based Medical Systems (CBMS 2021), 2021
Publisher: IEEE
DOI: 10.1109/cbms52027.2021.00086