arXiv subjects

Marcel Kirchner

Publications and source records attributed to Marcel Kirchner.

2 recordsLinked to original sources

arXiv2026

Characterization of DLBCL cell of origin-phenotypes based on tumor microenvironment features

Diffuse large B-cell lymphoma (DLBCL) is an aggressive form of non-Hodgkin lymphoma with a high recurrence rate. The molecular profiling of DLBCL tumors culminated in several immunohistochemistry algorithms for prognostic stratification. Among those, the Hans classifier is widely used for classifying DLBCL into germinal center B-cell-like (GCB) and non-germinal center/activated B-cell-like (non-GCB/ABC) subtypes. The Hans classifier primarily evaluates protein expression of tumor-associated markers, however the tumor microenvironment (TME) of DLBCL includes a myriad of immune and stromal cells, cytokines, and extracellular matrix components that contribute to tumor growth, immune evasion, and recurrence rate. Although the Hans classifier provides a practical method for subtype identification, incorporation of TME information may improve risk stratification and further refine patient groups. Here, we present an unbiased deep learning-based approach to extract meaningful features from TME of DLBCL tumors for the automated processing and analysis of multiplexed images of a DLBCL patient cohort. Our pipeline quantifies a range of features that describe tumor sample cell composition, morphology, and its spatial organization. We point to alterations in the proportions of several cell populations between GCB and ABC tumors including increased immune cell proportions of the ABC and its preferential interaction with the M2-macrophages. Our analysis offers an in-depth characterization of the DLBCL subtypes and is exemplary of how our pipeline can be used for detailed quantitative analysis of a tumor and its subtypes.

q-bio.QM↗

arXiv2021

QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy

In April 2020, the QUality Assessment and REProducibility for Instruments and Images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models, and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper 1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; 2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers, and observers of such; 3) outlines the current actions of the QUAREP-LiMi initiative, and 4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.

q-bio.OT↗