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Research Projects

Current Projects

  • Intelligent MR Diagnosis of the Liver by Linking Model and Data-driven Processes (iDELIVER)

    (Third Party Funds Single)

    Term: August 3, 2020 - March 31, 2023
    Funding source: Bundesministerium für Bildung und Forschung (BMBF)

    The project examines the use and further development of machine learning methods for MR image reconstruction and for the classification of liver lesions. Based on a comparison model and data-driven image reconstruction methods, these are to be systematically linked in order to enable high acceleration without sacrificing diagnostic value. In addition to the design of suitable networks, research should also be carried out to determine whether metadata (e.g. age of the patient) can be incorporated into the reconstruction. Furthermore, suitable classification algorithms on an image basis are to be developed and the potential of direct classification on the raw data is to be explored. In the long term, intelligent MR diagnostics can significantly increase the efficiency of use of MR hardware, guarantee better patient care and set new impulses in medical technology.

  • Molecular Assessment of Signatures ChAracterizing the Remission of Arthritis

    (Third Party Funds Single)

    Term: April 1, 2020 - September 30, 2021
    Funding source: Bundesministerium für Bildung und Forschung (BMBF)

    MASCARA zielt auf eine detaillierte, molekulare Charakterisierung der Remission bei Arthritis ab. Das Projekt basiert auf der kombinierten klinischen und technischen Erfahrung von Rheumatologen, Radiologen, Medizinphysikern, Nuklearmedizinern, Gastroenterologen, grundlagenwissenschaftlichen Biologen und Informatikern und verbindet fünf akademische Fachzentren in Deutschland. Das Projekt adressiert 1) den Umstand der zunehmenden Zahl von Arthritis Patienten in Remission, 2) die Herausforderungen, eine effektive Unterdrückung der Entzündung von einer Heilung zu unterscheiden und 3) das begrenzte Wissen über die Gewebeveränderungen in den Gelenken von Patienten mit Arthritis. MASCARA wird auf der Grundlage vorläufiger Daten vier wichtige mechanistische Bereiche (immunstoffwechselbedingte Veränderungen, mesenchymale Gewebereaktionen, residente Immunzellen und Schutzfunktion des Darms) untersuchen, die gemeinsam den molekularen Zustand der Remission bestimmen. Das Projekt zielt auf die Sammlung von Synovialbiopsien und die anschließende Gewebeanalyse bei Patienten mit aktiver Arthritis und Patienten in Remission ab. Die Gewebeanalysen umfassen (Einzelzell)-mRNA-Sequenzierung, Massenzytometrie sowie die Messung von Immunmetaboliten und werden durch molekulare Bildgebungsverfahren wie CEST-MRT und FAPI-PET ergänzt. Sämtliche Daten, die in dem Vorhaben generiert werden, werden in einem bereits bestehenden Datenbanksystem mit den Daten der anderen Partner zusammengeführt und gespeichert. Das Zusammenführen der Daten soll – mit Hilfe von maschinellem Lernen – krankheitsspezifische und mit der Krankheitsaktivität verbundene Mustermatrizen identifizieren.

  • Deep-Learning basierte Segmentierung und Landmarkendetektion auf Röntgenbildern für unfallchirurgische Eingriffe

    (Third Party Funds Single)

    Term: since May 6, 2019
    Funding source: Siemens AG
  • Improving multi-modal quantitative SPECT with Deep Learning approaches to optimize image reconstruction and extraction of medical information

    (Non-FAU Project)

    Term: April 1, 2019 - April 30, 2022

    This project aims to improve multi-modal quantitative SPECT with Deep Learning approaches to optimize image reconstruction and extraction of medical information. Such improvements include noise reduction and artifact removal from data acquired in SPECT.

  • Advancing osteoporosis medicine by observing bone microstructure and remodelling using a four-dimensional nanoscope

    (Third Party Funds Single)

    Term: April 1, 2019 - March 31, 2025
    Funding source: European Research Council (ERC)
    URL: https://cordis.europa.eu/project/id/810316

    Due to Europe's ageing society, there has been a dramatic increase in the occurrence of osteoporosis (OP) and related diseases. Sufferers have an impaired quality of life, and there is a considerable cost to society associated with the consequent loss of productivity and injuries. The current understanding of this disease needs to be revolutionized, but study has been hampered by a lack of means to properly characterize bone structure, remodeling dynamics and vascular activity. This project, 4D nanoSCOPE, will develop tools and techniques to permit time-resolved imaging and characterization of bone in three spatial dimensions (both in vitro and in vivo), thereby permitting monitoring of bone remodeling and revolutionizing the understanding of bone morphology and its function.

    To advance the field, in vivo high-resolution studies of living bone are essential, but existing techniques are not capable of this. By combining state-of-the art image processing software with innovative 'precision learning' software methods to compensate for artefacts (due e.g. to the subject breathing or twitching), and innovative X-ray microscope hardware which together will greatly speed up image acquisition (aim is a factor of 100), the project will enable in vivo X-ray microscopy studies of small animals (mice) for the first time. The time series of three-dimensional X-ray images will be complemented by correlative microscopy and spectroscopy techniques (with new software) to thoroughly characterize (serial) bone sections ex vivo.

    The resulting three-dimensional datasets combining structure, chemical composition, transport velocities and local strength will be used by the PIs and international collaborators to study the dynamics of bone microstructure. This will be the first time that this has been possible in living creatures, enabling an assessment of the effects on bone of age, hormones, inflammation and treatment.

  • Deep Learning based Noise Reduction for Hearing Aids

    (Third Party Funds Single)

    Term: February 1, 2019 - January 31, 2022
    Funding source: Industrie
     

    Reduction of unwanted environmental noises is an important feature of today’s hearing aids, which is why noise reduction is nowadays included in almost every commercially available device. The majority of these algorithms, however, is restricted to the reduction of stationary noises. Due to the large number of different background noises in daily situations, it is hard to heuristically cover the complete solution space of noise reduction schemes. Deep learning-based algorithms pose a possible solution to this dilemma, however, they sometimes lack robustness and applicability in the strict context of hearing aids.
    In this project we investigate several deep learning.based methods for noise reduction under the constraints of modern hearing aids. This involves a low latency processing as well as the employing a hearing instrument-grade filter bank. Another important aim is the robustness of the developed methods. Therefore, the methods will be applied to real-world noise signals recorded with hearing instruments.

  • Digitalization in clinical settings using graph databases

    (Non-FAU Project)

    Term: since October 1, 2018
    Funding source: Bayerisches Staatsministerium für Wirtschaft, Landesentwicklung und Energie (StMWi) (seit 2018)

    In clinical settings, different data is stored in different systems. These data are very heterogeneous, but still highly interconnected. Graph databases are a good fit for this kind of data: they contain heterogeneous "data nodes" which can be connected to each other. The basic question is now if and how clinical data can be used in a graph database, most importantly how clinical staff can profit from this approach. Possible scenarios are a graphical user interface for clinical staff for easier access to required information or an interface for evaluation and analysis to answer more complex questions. (e.g., "Were there similar patients to this patient? How were they treated?")

  • Modelling the progression of neurological diseases

    (Third Party Funds Group – Sub project)

    Overall project: Training Network on Automatic Processing of PAthological Speech
    Term: since May 1, 2018
    Funding source: Innovative Training Networks (ITN)

    Develop speech technology that can allow unobtrusive monitoring of many kinds of neurological diseases. The state of a patient can degrade slowly between medical check-ups. We want to track the state of a patient unobtrusively without the feeling of constant supervision. At the same time the privacy of the patient has to be respected. We will concentrate on PD and thus on acoustic cues of changes. The algorithms should run on a smartphone, track acoustic changes during regular phone conversations over time and thus have to be low-resource. No speech recognition will be used and only some analysis parameters of the conversation are stored on the phone and transferred to the server.

  • Deep Learning Applied to Animal Linguistics

    (FAU Funds)

    Term: April 1, 2018 - April 1, 2022
    Deep Learning Applied to Animal Linguistics in particular the analysis of underwater audio recordings of marine animals (killer whales):

    For marine biologists, the interpretation and understanding of underwater audio recordings is essential. Based on such recordings, possible conclusions about behaviour, communication and social interactions of marine animals can be made. Despite a large number of biological studies on the subject of orca vocalizations, it is still difficult to recognize a structure or semantic/syntactic significance of orca signals in order to be able to derive any language and/or behavioral patterns. Due to a lack of techniques and computational tools, hundreds of hours of underwater recordings are still manually verified by marine biologists in order to detect potential orca vocalizations. In a post process these identified orca signals are analyzed and categorized. One of the main goals is to provide a robust and automatic method which is able to automatically detect orca calls within underwater audio recordings. A robust detection of orca signals is the baseline for any further and deeper analysis. Call type identification and classification based on pre-segmented signals can be used in order to derive semantic and syntactic patterns. In connection with the associated situational video recordings and behaviour descriptions (provided by several researchers on site) can provide potential information about communication (kind of a language model) and behaviors (e.g. hunting, socializing). Furthermore, orca signal detection can be used in conjunction with a localization software in order to provide researchers on the field with a more efficient way of searching the animals as well as individual recognition.

    For more information about the DeepAL project please contact christian.bergler@fau.de.

Former Projects from 2017 on

  • Development of a digital therapy tool as an exercise supplement for speech disorders and facial paralysis

    (Third Party Funds Single)

    Term: June 1, 2017 - December 31, 2019
    Funding source: Bundesministerium für Wirtschaft und Technologie (BMWi)

    Dysarthrien sind neurologisch bedingte, erworbene Störungen des Sprechens. Dabei sind vor allem die Koordination und Ausführung der Sprechbewegungen, aber auch die Mimik betroffen. Besonders häufig tritt eine Dysarthrie nach einem Schlaganfall, Schädel-Hirn-Trauma oder bei neurologischen Erkrankungen wie Parkinson auf.

    Ähnlich wie in allen Sprechtherapien erfordert auch die Behandlung der Dysarthrie ein intensives Training. Anhaltende Effekte der Dysarthrie-Therapie stellen sich deshalb nur nach einem umfangreichen Behandlungsprogramm über mehrere Wochen hinweg ein. Bisher gibt es jedoch kaum Möglichkeiten zur Selbstkontrolle für Patienten noch therapeutische Anleitung in einem häuslichen Umfeld. Auch die Rückmeldung an Ärzte / Therapeuten über den Therapieerfolg ist eher lückenhaft.

    Das Projekt DysarTrain setzt genau hier an und will ein interaktives, digitales Therapieangebot für das Sprechtraining schaffen, damit Patienten ihre Übungen im häuslichen Umfeld durchführen können. In enger Abstimmung mit Ärzten, Therapeuten und Patienten werden zuerst die passenden Therapieinhalte zur Behandlung von Dysarthrien ausgewählt und digitalisiert. In einem zweiten Schritt wird eine Therapieplattform mit den geeigneten Kommunikations-, Interaktions- und Supervisionsfunktionen aufgebaut. Für die Durchführung des Trainings werden anschließend Assistenzfunktionen und Feedbackmechanismen entwickelt. Das Programm soll automatisch rückmelden, ob eine Übung gut absolviert wurde und was ggf. noch verbessert werden kann. Eine automatisierte Auswertung der Therapiedaten erlaubt es Ärzten und Therapeuten, die Therapieform auf möglichst einfache Weise zu individualisieren und an den jeweiligen Therapiestand anzupassen. Dieses Angebot wird mit Ärzten, Therapeuten und Patienten in den Behandlungsprozess integriert und evaluiert.

  • Development of multi-modal, multi-scale imaging framework for the early diagnosis of breast cancer

    (FAU Funds)

    Term: March 1, 2017 - June 30, 2020

    Breast cancer is the leading cause of cancer related deaths in women, the second most common cancer worldwide. The development and progression of breast cancer is a dynamic biological and evolutionary process. It involves a composite organ system, with transcriptome shaped by gene aberrations, epigenetic changes, the cellular biological context, and environmental influences. Breast cancer growth and response to treatment has a number of characteristics that are specific to the individual patient, for example the response of the immune system and the interaction with the neighboring tissue. The overall complexity of breast cancer is the main cause for the current, unsatisfying understanding of its development and the patient’s therapy response. Although recent precision medicine approaches, including genomic characterization and immunotherapies, have shown clear improvements with regard to prognosis, the right treatment of this disease remains a serious challenge. The vision of the BIG-THERA team is to improve individualized breast cancer diagnostics and therapy, with the ultimate goal of extending the life expectancy of breast cancer sufferers. Our primary contribution in this regard is developing a multi-modal, multi-scale framework for the early diagnosis of the molecular sub-types of breast cancer, in a manner that supplements the clinical diagnostic workflow and enables the early identification of patients compatible with specific immunotherapeutic solutions.

  • Digital Pathology - New Approaches to the Automated Image Analysis of Histologic Slides

    (Own Funds)

    Term: since January 16, 2017

    The pathologist is still the gold standard in the diagnosis of diseases in tissue slides. Due to its human nature, the pathologist is on one side able to flexibly adapt to the high morphological and technical variability of histologic slides but of limited objectivity due to cognitive and visual traps.

    In diverse project we are applying and validating currently available tools and solutions in digital pathology but are also developing new solution in automated image analysis to complement and improve the pathologist especially in areas of quantitative image analysis.

  • Deep Learning for Multi-modal Cardiac MR Image Analysis and Quantification

    (Third Party Funds Single)

    Term: January 1, 2017 - May 1, 2020
    Funding source: Deutscher Akademischer Austauschdienst (DAAD)

    Cardiovascular diseases (CVDs) and other cardiac pathologies are the leading cause of death in Europe and the USA. Timely diagnosis and post-treatment follow-ups are imperative for improving survival rates and delivering high-quality patient care. These steps rely heavily on numerous cardiac imaging modalities, which include CT (computerized tomography), coronary angiography and cardiac MRI. Cardiac MRI is a non-invasive imaging modality used to detect and monitor cardiovascular diseases. Consequently, quantitative assessment and analysis of cardiac images is vital for diagnosis and devising suitable treatments. The reliability of quantitative metrics that characterize cardiac functions such as, myocardial deformation and ventricular ejection fraction, depends heavily on the precision of the heart chamber segmentation and quantification. In this project, we aim to investigate deep learning methods to improve the diagnosis and prognosis for CVDs,