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Biology subjects

Greene, R.

Publications and source records attributed to Greene, R..

2 recordsLinked to original sources

UnitRefine: A Community Toolbox for Automated Spike Sorting Curation

High-density electrophysiology simultaneously captures the activity from hundreds of neurons, but isolating single-unit activity still relies on slow and subjective manual curation. As datasets keep increasing, this poses a major bottleneck in the field. We therefore developed UnitRefine, a classification toolbox that automates curation by training various machine-learning models directly on human expert annotations. Fully integrated in the SpikeInterface ecosystem, UnitRefine combines established and novel quality metrics, cascading classification and comprehensive hyperparameter search to provide optimized models for different applications. UnitRefine achieves human-level performance across diverse datasets, spanning species, probe types, and laboratories, including recordings from mice, rats, mole rats, primates, and human patients. Applied to a large brain-wide dataset, UnitRefine doubled single unit yield and improved behavioral decoding performance. A streamlined graphical interface allows models to be fine-tuned to new datasets and shared via the Hugging Face Hub, enabling broad adoption and community-driven improvement of automated curation workflows.

neuroscience↗

A novel in vitro 3D cancer model based on modular tissue engineering approach

An emerging tool to better recapitulate the complexity of tumor biology in vitro is 3D culture models. Here, we describe a free-floating collagen-based hydrogel system with embedded cancer cells, called microtissues. The microtissues are based on the well-established modular tissue engineering method. They mimic the natural development of the tumor microenvironment, with features such as hypoxia and treatment resistance. To demonstrate the utility of microtissues as a 3D tumor model system, triple negative breast cancer cells were cultured using this method and were shown to maintain cell viability and proliferation with minimal cell death, along with mimicking natural emergence of tumor properties such as, a hypoxic core. Furthermore, by screening the model with commonly used anti-breast cancer chemotherapeutics, we observed drug resistance to concentrations which are largely in accordance with the used doses in the clinics. Therefore, our model offers the opportunity to naturally reproduce fundamental features of a tumor in vitro, leading to emergence of a similar cell reprogramming which is responsible for clinical drug resistance.

cancer biology↗