Biology subjects

Hirata-Miyasaki, E.

Publications and source records attributed to Hirata-Miyasaki, E..

3 recordsLinked to original sources

bioRxiv2024

High-speed 3D Imaging with 25-Camera Multifocus Microscope

We here report an aberration-corrected 25-plane camera array Multifocus microscope (M25) for high-speed, high-resolution wide-field optical microscopy in three spatial dimensions (3D). We demonstrate live imaging of 25-plane 3D volumes of up to 180x180x50um at >100 volumes per second. 3D data is recorded simultaneously by an array of 25 small, sensitive, synchronized machine-vision cameras. M25 employs aberration-corrected Multifocus microscopy--an optical method where diffractive Fourier optics are used for multiplexing and refocusing light-- with a simplified design for chromatic dispersion correction where a corrective diffractive gratings is placed on each camera in the array. This elegant architecture for chromatic correction will be applicable in a broad range of diffractive imaging applications. M25 is a powerful optical tool for high-speed 3D microscopy in that it allows both non-invasive, label-free bright-field and highly sensitive fluorescence microscopy. We showcase M25 capabilities in 3D particle tracking, bright-field, and fluorescence imaging in D. melanogaster, and locomotion and neural activity studies in C. elegans.

neuroscience↗

bioRxiv2024

Ultrack: pushing the limits of cell tracking across biological scales

Tracking live cells across 2D, 3D, and multi-channel time-lapse recordings is crucial for understanding tissue-scale biological processes. Despite advancements in imaging technology, achieving accurate cell tracking remains challenging, particularly in complex and crowded tissues where cell segmentation is often ambiguous. We present Ultrack, a versatile and scalable cell-tracking method that tackles this challenge by considering candidate segmentations derived from multiple algorithms and parameter sets. Ultrack employs temporal consistency to select optimal segments, ensuring robust performance even under segmentation uncertainty. We validate our method on diverse datasets, including terabyte-scale developmental time-lapses of zebrafish, fruit fly, and nematode embryos, as well as multi-color and label-free cellular imaging. We show that Ultrack achieves state-of-the-art performance on the Cell Tracking Challenge and demonstrates superior accuracy in tracking densely packed embryonic cells over extended periods. Moreover, we propose an approach to tracking validation via dual-channel sparse labeling that enables high-fidelity ground truth generation, pushing the boundaries of long-term cell tracking assessment. Our method is freely available as a Python package with Fiji and napari plugins and can be deployed in a high-performance computing environment, facilitating widespread adoption by the research community.

developmental biology↗

bioRxiv2023

Mantis: high-throughput 4D imaging and analysis of the molecular and physical architecture of cells

High-throughput dynamic imaging of cells and organelles is essential for understanding complex cellular responses. We report Mantis, a high-throughput 4D microscope that integrates two complementary, gentle, live-cell imaging technologies: remote-refocus label-free microscopy and oblique light-sheet fluorescence microscopy. Additionally, we report shrimPy, an open-source software for high-throughput imaging, deconvolution, and single-cell phenotyping of 4D data. Using Mantis and shrimPy, we achieved high-content correlative imaging of molecular dynamics and the physical architecture of 20 cell lines every 15 minutes over 7.5 hours. This platform also facilitated detailed measurements of the impacts of viral infection on the architecture of host cells and host proteins. The Mantis platform can enable high-throughput profiling of intracellular dynamics, long-term imaging and analysis of cellular responses to perturbations, and live-cell optical screens to dissect gene regulatory networks. Significance StatementUnderstanding the dynamics and interactions of cellular components is crucial for biological research and drug discovery. Current dynamic fluorescence microscopy methods can only image a few fluorescent labels, providing a limited view of these complex processes. We developed Mantis, a high-throughput 3D microscope that maps interactions among components of dynamic cell systems. Mantis combines light-sheet fluorescence imaging of multiple fluorophores with quantitative label-free microscopy and is complemented by shrimPy, our open-source software for high-throughput data acquisition and high-performance analysis. Mantis enabled simultaneous 3D time-lapse imaging of 20 cell lines and quantitative analysis of responses to perturbations like viral infection at single-cell resolution. This approach can accelerate the analysis of cellular dynamics and image-based drug discovery.

cell biology↗