Biology subjects

Habermann, S.

Publications and source records attributed to Habermann, S..

3 recordsLinked to original sources

bioRxiv2026

3D Reconstruction of Nanoparticle Distribution in Tumor Spheroids with Volume Electron Microscopy

AO_SCPLOWBSTRACTC_SCPLOWSpatially resolved characterization of nanomaterial (NM) distribution within cellular ultrastructure is essential for understanding NM fate and activity in biological systems. Volume electron microscopy (vEM) is uniquely positioned to address this challenge, yet fully documented quantitative pipelines that simultaneously segment NMs and cellular structures remain scarce. Here, an end-to-end analytical pipeline is presented based on the example of serial block-face scanning electron microscopy (SBF-SEM) data of tumor spheroids containing nanoparticles (NPs). A hybrid segmentation strategy is adopted: a fine-tuned Cellpose-SAM model for cells and nuclei, and an empirical Bayes approach for AuNPs. The fine-tuned model outperforms both the pre-trained baseline and benchmark experiments in Amira, and shows good generalization to 2D EM datasets of varying sample types, suggesting potential as a general-purpose segmentation model for electron microscopy. Full 3D reconstruction of NP distributions reveals preferential clustering in the perinuclear region, with a median nucleus-to-NP distance of 2.57 {micro}m and NM uptake spanning several orders of magnitude across cells. Furthermore, morphological analysis of segmented cells and nuclei using 3D shape descriptors and local curvature metrics provides quantitative access to features inaccessible from single sections. Together, these results establish a reproducible, open framework for the joint quantitative analysis of NM distribution and cellular morphology in vEM data.

bioinformatics↗

bioRxiv2025

Nanoparticle Metal Mass Uptake Governs Radiosensitizing Efficacy Across 2D, 3D, and In Vivo Models

Despite extensive efforts to develop nanoparticle-based radioenhancers, clinical translation remains limited, partly due to the lack of physiologically relevant in vitro models. To address this gap, we developed a 3D spheroid model of head and neck cancer using FaDu cells and compared it directly to a corresponding in vivo model in a radiotherapy setting. The spheroids exhibited key tumor-like features, including the formation of a hypoxic core and growth kinetics comparable to in vivo tumors. Importantly, the model allowed for long-term monitoring of tumor growth and radiation response. Upon X-ray irradiation, dose-response behavior in spheroids mirrored that observed in vivo. Furthermore, TiO2, HfO2, and Au nanoparticles demonstrated consistent radiosensitization effects in both systems when matched for uptake mass. In contrast, conventional 2D clonogenic assays failed to predict in vivo performance, likely due to their lower radioresistance and unrealistic nanoparticle exposure conditions. This study introduces a robust, scalable, and clinically compatible 3D in vitro platform for preclinical screening of nanoparticle radioenhancers. The system may offer streamlining of development pipelines and support the 3R principles of reduction, replacement, and refinement in radiation oncology research.

cancer biology↗

bioRxiv2024

Cathodoluminescent and Characteristic X-ray-emissive Rare-Earth-doped Core/Shell Immunolabels for Spectromicroscopic Analysis of Cell Surface Receptors

Understanding the localization and the interactions of biomolecules at the nanoscale and in the cellular context remains challenging. Electron microscopy (EM) as a non-Abbe limited technique gives access to the cellular ultra-structure yet results in grey-scale images and averts unambiguous (co-)localization of biomolecules. Multimodal nanoparticle-based immunolabels for correlative cathodoluminescence electron microscopy (CCLEM) and energy-dispersive X-ray spectromicroscopy (EDX-SM) are presented. The single-particle STEM-cathodoluminescence (CL) and characteristic X-ray emissivity of sub-20 nm lanthanide-doped nanoparticles were exploited as unique spectral fingerprints for precise localization and label identification. To maximize the nanoparticle brightness, lanthanides were incorporated in a low-phonon host lattice and separated from the environment using a passivating shell. The core/shell nanoparticles were then functionalized with either folic (terbium-doped) or caffeic acid (europium-doped). Their potential for immunolabeling was successfully demonstrated using HeLa cells expressing different surface receptors that bind to folic or caffeic acid, respectively. Both particle populations showed single-particle CL emission along with a distinctive energy-dispersive X-ray signal, with the latter enabling colour-based localization of receptors within swift imaging times well below 2 mins per {micro}m2 while offering high resolution with a pixel size of 2.78 nm. Taken together, these results open a route to color immunolabelling based on electron spectromicroscopy. Table of Contents O_FIG O_LINKSMALLFIG WIDTH=184 HEIGHT=200 SRC="FIGDIR/small/585848v1_ufig1.gif" ALT="Figure 1"> View larger version (74K): org.highwire.dtl.DTLVardef@1f7c2d3org.highwire.dtl.DTLVardef@117be1eorg.highwire.dtl.DTLVardef@1c2bab2org.highwire.dtl.DTLVardef@16f3677_HPS_FORMAT_FIGEXP M_FIG Small (sub-20 nm) lanthanide-doped nanoparticles were successfully utilized in electron microscopy to label biological structures and contextualize them in the cells ultrastructure. Leveraging unique energy-dispersive X-ray signatures, the nanoparticles location and doping-identity was easily and fast retrieved, demonstrating the methods potential to (co)-localize labels while supplying a holistic impression of the underlying processes, as entire cells could be mapped. C_FIG

bioengineering↗