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Wiestler, B.

Publications and source records attributed to Wiestler, B..

4 recordsLinked to original sources

MedMCP: An Open Agentic Ecosystem for Medical Imaging Workflows

Deep learning has driven rapid progress in medical image analysis, with methods for tasks such as organ segmentation, anomaly detection, and radiology report generation now matching or surpassing expert performance on several benchmarks. While many methods are released as open source, their routine adoption by clinicians and medical researchers remains limited. The bottleneck is not a lack of capable tools, but the absence of infrastructure to make them accessible to non-technical users. To break this barrier, we present MedMCP, an agentic framework that solves this last-mile problem along two axes: (1) a local agentic workspace that lets users apply state-of-the-art image analysis methods through natural language, and (2) a community-driven tool ecosystem that lets developers deploy and distribute capabilities as validated, independently testable servers. MedMCP enforces a strict orchestration-execution boundary in which a local language model translates user intent into workflow plans, while all image analysis is delegated to domain-specific tools. The framework runs entirely on-premise, every side-effecting operation passes through a human-in-the-loop permission gate, and a full provenance trail links each output to the tools, parameters, and inputs that produced it. An inspectable workspace lets users verify intermediate results rather than blindly trusting the agent, and completed sessions distill into deterministic, shareable workflows that re-execute without the agent, turning one-off interactions into reproducible analyses. This paper introduces the project's general idea and describes the design principles that guide its development. Beyond a single toolkit, we envision MedMCP as a community-driven platform where each contributed tool becomes easily accessible, compounding individual efforts into shared capability.

bioinformatics↗

Epigenetic neural glioblastoma enhances synaptic integration and predicts therapeutic vulnerability

Neural-tumor interactions drive glioma growth as evidenced in preclinical models, but clinical validation is nascent. We present an epigenetically defined neural signature of glioblastoma that independently affects patients survival. We use reference signatures of neural cells to deconvolve tumor DNA and classify samples into low- or high-neural tumors. High-neural glioblastomas exhibit hypomethylated CpG sites and upregulation of genes associated with synaptic integration. Single-cell transcriptomic analysis reveals high abundance of stem cell-like malignant cells classified as oligodendrocyte precursor and neural precursor cell-like in high-neural glioblastoma. High-neural glioblastoma cells engender neuron-to-glioma synapse formation in vitro and in vivo and show an unfavorable survival after xenografting. In patients, a high-neural signature associates with decreased survival as well as increased functional connectivity and can be detected via DNA analytes and brain-derived neurotrophic factor in plasma. Our study presents an epigenetically defined malignant neural signature in high-grade gliomas that is prognostically relevant.

neuroscience↗

Virtual reality empowered deep learning analysis of brain activity

Tissue clearing and fluorescent microscopy are powerful tools for unbiased organ-scale protein expression studies. Critical for interpreting expression patterns of large imaged volumes are reliable quantification methods. Here, we present DELiVR a deep learning pipeline that uses virtual reality (VR)-generated training data to train deep neural networks, and quantify c-Fos as marker for neuronal activity in cleared mouse brains and map its expression at cellular resolution. VR annotation significantly accelerated the speed of generating training data compared to conventional 2D slice based annotation. DELiVR detects cells with much higher precision than current threshold-based pipelines, and provides an extensive toolbox for data visualization, inspection and comparison. We applied DELiVR to profile cancer-related mouse brain activity, and discovered a novel activation pattern that distinguishes between weight-stable cancer and cancer-associated weight loss. Thus, DELiVR provides a robust mouse brain analysis pipeline at cellular scale that can be used to study brain activity patterns in health and disease. The DELiVR software, Fiji plugin and documentation can be found at https://www.DISCOtechnologies.org/DELiVR/. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=169 SRC="FIGDIR/small/540970v1_ufig1.gif" ALT="Figure 1"> View larger version (66K): org.highwire.dtl.DTLVardef@172d5bforg.highwire.dtl.DTLVardef@2f1d80org.highwire.dtl.DTLVardef@139e7a0org.highwire.dtl.DTLVardef@95dce1_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDELiVR detects labelled cells in cleared brains with deep learning C_LIO_LIDELiVR is trained by annotating ground-truth data in virtual reality (VR) C_LIO_LIDELiVR is launched via a FIJI plugin anywhere from PCs to clusters C_LIO_LIUsing DELiVR, we found new brain activity patterns in weight-stable vs. cachectic cancer C_LI Supplementary Videos can be seen at: https://www.DISCOtechnologies.org/DELiVR/

bioinformatics↗

Pre-operarative Multivariate Connectome Analysis for Glioma Patients

Recent advances in neuroimaging have allowed the use of network analysis to study the brain in a system-based approach. A system-based analysis of gliomas can shed light on mechanisms underlying neuronal connectivity and plasticity and the recovery process, and it could support surgical decision-making. Surgery has been shifting from image-guided surgery to a functional mapping-guided resection where several structural and functional modalities are used. However, reliable identification of eloquent areas during planning of surgical resection is still a challenge. Pre-operative language mapping performed by navigated transcranial magnetic stimulation (nTMS) is of great value as it elucidates functional cortical organization, which might be different from patient to patient due to the heterogeneity of the lesions and individual plasticity. In this paper we propose the construction of an \"effective\" speech network used for surgical decision making. This is achieved by mapping functionally relevant areas identified by nTMS on tractography-based connectomics. Subsequently we compute graph metrics on the identified speech networks of patients who show preoperative aphasia aiming to identify relevant differences between graph metrics in patients with and without preoperative aphasia. Lastly, the validity of the speech networks is examined by checking the involved graph communities.

neuroscience↗