Cell Painting: a decade of discovery and innovation in cellular imaging

Nature Methods, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 5, 2024

Language: Английский

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Flexible and stretchable bioelectronics for organoids

Med-X, Journal Year: 2025, Volume and Issue: 3(1)

Published: Feb. 1, 2025

Abstract Organoids have gained significant interest due to their ability recapitulate the structural, molecular, and functional complexity of corresponding organs. While methods been developed characterize benchmark organoid structural molecular properties, capturing development maturation organoids remains challenging. To address this, multifunctional bioelectronics for interfacing with has actively pursued. However, conventional electronics face limitations in achieving recording control across entire three-dimensional (3D) volume a long-term stable manner large morphological cellular composition changes during development. In this review, we first discuss application interfacing. We then focus on flexible stretchable designed create organoid/electronics hybrids chronically interfaces. also review recent advancements charting multimodal cell activities throughout Furthermore, explore integration other characterization modalities comprehensive cells within 3D tissues. Finally, potential integrating artificial intelligence into system through embedded electronics, harnessing biosymbiotic computational systems. These could provide valuable tools characterizing maturation, establishing patient-specific models, developing therapeutic opportunities, exploring novel strategies. Graphical abstract

Language: Английский

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HIPPIE: A Multimodal Deep Learning Model for Electrophysiological Classification of Neurons

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: March 15, 2025

Abstract Extracellular electrophysiological recordings present unique computational challenges for neuronal classification due to noise, technical variability, and batch effects across experimental systems. We introduce HIPPIE (High-dimensional Interpretation of Physiological Patterns In recordings), a deep learning framework that combines self-supervised pretraining on unlabeled datasets with supervised fine-tuning classify neurons from extracellular recordings. Using conditional convolutional joint autoencoders, learns robust, technology-adjusted representations waveforms spiking dynamics. This model can be applied clustering diverse biological cultures technologies. validated both in vivo mouse vitro brain slices, where it demonstrated superior performance over other unsupervised methods cell-type discrimination aligned closely anatomically defined classes. Its latent space organizes along gradients, while enabling individual corrected alignment experiments. establishes general systematically decoding diversity native engineered

Language: Английский

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Special Mini-Issue: Quantitative methods to decipher cellular heterogeneity – from single-cell to spatial omic methods

Biophysical Reviews, Journal Year: 2024, Volume and Issue: 16(1), P. 11 - 12

Published: Jan. 30, 2024

Language: Английский

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Biophysical Reviews: peering into 2024

Biophysical Reviews, Journal Year: 2024, Volume and Issue: 16(1), P. 1 - 7

Published: Feb. 1, 2024

Language: Английский

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Integration of hyperspectral imaging and transcriptomics from individual cells with HyperSeq

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 30, 2024

Abstract Microscopy and omics are complementary approaches to probe the molecular state of cells in health disease, combining granularity with scalability. While important advances have been achieved over last decade each area, integrating both imaging- sequencing-based assays on same cell has proven challenging. In this study, a new approach called HyperSeq that combines hyperspectral autofluorescence imaging transcriptomics is demonstrated. was applied Michigan Cancer Foundation 7 (MCF-7) breast cancer identified subpopulation exhibiting bright rings at plasma membrane optical channel 13 ( λ ex = 431 nm, em 594 nm). Correlating presence ring gene expression indicated ringed more likely express hallmark genes apoptosis less associated ATP production. Further, correlation morphology suggested multiple members spliceosome were downregulated larger MCF-7 cells. Multiple evenly expressed across sizes but also exhibited higher usage specific exons or smaller Finally, between fluorescence within spectral range Nicotinamide adenine dinucleotide hydrogen (NADH) provided insight into metabolic states These observations link cell’s spectrum its internal state, demonstrating utility study biology single resolution by spectral, morphological transcriptomic analyses single, streamlined workflow.

Language: Английский

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Gene Expression, Morphology, and Electrophysiology During the Dynamic Development of Human Induced Pluripotent Stem Cell-Derived Atrial- and Ventricular-Like Cardiomyocytes [Letter]

Biologics, Journal Year: 2024, Volume and Issue: Volume 18, P. 145 - 146

Published: June 1, 2024

Language: Английский

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