A5046266487- Cell Image Analysis Techniques
- Medical Imaging Techniques and Applications
- Advanced Fluorescence Microscopy Techniques
- Single-cell and spatial transcriptomics
- Cancer, Hypoxia, and Metabolism
- Radiomics and Machine Learning in Medical Imaging
- Head and Neck Cancer Studies
- Genetics, Bioinformatics, and Biomedical Research
- Advanced Radiotherapy Techniques
- Medical Image Segmentation Techniques
- Radiation Therapy and Dosimetry
- Advanced Electron Microscopy Techniques and Applications
- Lung Cancer Diagnosis and Treatment
- Diet and metabolism studies
- Gastrointestinal motility and disorders
- Congenital gastrointestinal and neural anomalies
- Electron and X-Ray Spectroscopy Techniques
- Scientific Computing and Data Management
- Advanced Neural Network Applications
- AI in cancer detection
- Advanced Image and Video Retrieval Techniques
- Image Processing Techniques and Applications
- Computer Graphics and Visualization Techniques
- Insect and Arachnid Ecology and Behavior
- Distributed and Parallel Computing Systems
TU Dresden
2016-2025
Leipzig University
2023-2025
Center for Scalable Data Analytics and Artificial Intelligence
2024
Max Planck Institute of Molecular Cell Biology and Genetics
2016-2023
Center for Systems Biology Dresden
2019-2022
Immanuel Klinikum Bernau
2019
OncoRay
2011-2019
Helmholtz-Zentrum Dresden-Rossendorf
2015-2019
University Hospital Carl Gustav Carus
2012-2019
Klinikum Brandenburg
2018
Accurate detection and segmentation of cell nuclei in volumetric (3D) fluorescence microscopy datasets is an important step many biomedical research projects. Although automated methods for these tasks exist, they often struggle images with low signal-to-noise ratios and/or dense packing nuclei. It was recently shown 2D that issues can be alleviated by training a neural network to directly predict suitable shape representation (star-convex polygon) In this paper, we adopt extend approach 3D...
PurposeTo explore in a prospective trial the prognostic value of hypoxia imaging before and during radiochemotherapy patients with locally advanced head neck cancer.Patients methodsTwenty-five stage III/IV cancer were investigated [18F]-fluoromisonidazole (FMISO) PET/CT at four time points (baseline, 8–10 Gy, 18–20 Gy,50–60 Gy). FMISO image parameters extracted including maximum-tumour-to-background (TBRmax) thresholded volume different TBR ratios. CT baseline FDG-PET/CT also included....
We present LABKIT, a user-friendly Fiji plugin for the segmentation of microscopy image data. It offers easy to use manual and automated routines that can be rapidly applied single- multi-channel images as well timelapse movies in 2D or 3D. LABKIT is specifically designed work efficiently on big data enables users consumer laptops conveniently with multiple-terabyte images. This efficiency achieved by using ImgLib2 BigDataViewer memory efficient fast implementation random forest based pixel...
ABSTRACT Elucidating the developmental processes of organisms requires a comprehensive understanding cellular lineages in spatial, temporal, and molecular domains. In this study, we introduce Zebrahub, dynamic atlas zebrafish embryonic development that integrates single-cell sequencing time course data with lineage reconstructions facilitated by light-sheet microscopy. This offers high-resolution in-depth insights into development, achieved through individual embryos across ten stages,...
Abstract Many animal embryos pull and close an epithelial sheet around the ellipsoidal egg surface during a gastrulation process known as epiboly. The ovoidal geometry dictates that first expands subsequently compacts. Moreover, spreading epithelium is mechanically stressed this stress needs to be released. Here we show extraembryonic tissue (serosa) epiboly in insect Tribolium castaneum , non-proliferative serosa becomes regionalized into solid-like dorsal region with larger non-rearranging...
Light microscopy enables researchers to observe cellular mechanisms with high spatial and temporal resolution. However, the increasing complexity of current imaging technologies, coupled financial constraints potential users, hampers general accessibility reach cutting-edge microscopy. Open can address this issue by making well-designed well-documented hardware software solutions openly available a broad audience. In Comment, we provide definition open present recent projects in field. We...
Tumour hypoxia can be measured by FMISO-PET and negatively impacts local tumour control in patients with head neck squamous cell carcinoma (HNSCC) undergoing radiotherapy. The aim of this post hoc analysis a prospective clinical trial was to investigate the spatial variability FMISO hypoxic subvolumes during radio-chemotherapy co-localisation these volumes later recurrences as basis for individualised dose prescription trials escalation defined FMISO-PET. Sequential scans 12 (of 25)...
<ns3:p>Fast-paced innovations in imaging have resulted single systems producing exponential amounts of data to be analyzed. Computational methods developed computer science labs proven crucial for analyzing these an unbiased and efficient manner, reaching a prominent role most microscopy studies. Still, their use usually requires expertise bioimage analysis, accessibility life scientists has therefore become bottleneck.</ns3:p><ns3:p> Open-source software analysis disseminate computational...
Abstract Recent advances in microscopy imaging and image analysis motivate more institutes worldwide to establish dedicated core‐facilities for bioimage analysis. To maximise the benefits research groups at these gain from their core‐facilities, they should be established fit well into respective environment. In this article, we introduce common collaborator requests corresponding potential services can offer. We also discuss competing interests between targeted missions implementations of...
Background. To determine by treatment plan comparison differences in toxicity risk reduction for patients with head and neck squamous cell carcinoma (HNSCC) from proton therapy either used complete or sequential boost only.Materials methods. For 45 HNSCC patients, intensity-modulated photon (IMXT) (IMPT) plans were created including a dose escalation via simultaneous integrated one-step adaptation strategy after 25 fractions treatment. Dose accumulation was performed pure IMXT treatment,...
Preclinical in vivo studies using small animals are essential to develop new therapeutic options radiation oncology. Of particular interest orthotopic tumour models, which better reflect the clinical situation terms of growth patterns and microenvironmental parameters as well interplay tumours with surrounding normal tissues. Such models increase technical demands complexity preclinical local irradiation therapeutically relevant doses requires image-guided target localisation accurate beam...
Abstract Tooth classes are an innovation that has contributed to the evolutionary success of mammals. However, our understanding mechanisms by which tooth diversified remain limited. We use radiation noctilionoid bats show how developmental program evolved during adaptation new diet types. Combining morphological, and mathematical modeling approaches, we demonstrate develop through independent cascades deviate from classical models. diversification number size is driven jaw growth rate...
Interdisciplinary communities, such as the life-sciences, have a strong need for efficient knowledge-transfer. In our community, computer scientists, bioimage analysts and biologists frequently come together to train each other in quantitative microscopy data analysis. For these trainings, re-usable high-quality training materials can be key. We advocate publishing according FAIR principles: Materials must findable, openly accessible, stored interoperable file formats, most importantly made...
Abstract The expanding scale and complexity of microscopy image datasets require accelerated analytical workflows. NanoPyx meets this need through an adaptive framework enhanced for high-speed analysis. At the core NanoPyx, Liquid Engine dynamically generates optimized central processing unit graphics code variations, learning predicting fastest based on input data hardware. This data-driven optimization achieves considerably faster processing, becoming broadly relevant to reactive computing...
Mesenchymal stem cell therapy shows promising results for difficult-to-treat diseases, but standardized manufacturing requires robust quality control through automated confluence monitoring. While deep learning can automate estimation, research on cost-effective dataset curation and the role of foundation models in this task remains limited. We systematically investigate most effective strategies focusing active learning-based curation, goal-specific labeling, leveraging zero-shot inference....
Fluorescence lifetime imaging microscopy (FLIM) translates the duration of excited states fluorophores into information as additional source contrast in images biological samples. This offers possibility to separate particularly beneficial case similar excitation spectra. Here, we demonstrate distinction fluorescent molecules based on FLIM phasor analysis, called unmixing, live-cell using open-source software for analysis. We showcase two applications Caenorhabditis elegans a model system....
Abstract In the computational age, life-scientists often have to write Python code solve bio-image analysis (BIA) problems. Many of them not been formally trained in programming though. Code-generation, or coding assistance general, with Large Language Models (LLMs) can a clear impact on BIA. To best our knowledge, quality generated this domain has studied. We present quantitative benchmark estimate capability LLMs generate for solving common BIA tasks. Our currently consists 57...
The enteric nervous system (ENS) consists of an extensive network neurons and glial cells embedded within the wall gastrointestinal (GI) tract. Alterations in neuronal distribution function are strongly associated with GI dysfunction. Current methods for assessing suffer from undersampling, partly due to challenges imaging analyzing large tissue areas, operator bias manual analysis. We present Gut Analysis Toolbox (GAT), image analysis tool designed characterization their neurochemical...
[¹⁸F]Fluoromisonidazole positron emission tomography (FMISO-PET) is a non invasive imaging technique that can assist detecting intra tumour regions of hypoxia. FMISO-PET evinces comparatively low signal-to-noise-ratio (SNR) and may be acquired dynamically or after different uptake times post injection (p.i.). The aim this study was to identify, if static images two hours (MISO2) four (MISO4) p.i. reveal higher contrast.As part prospective trial, 23 patients with cancers the head neck...