Shuichi Onami

Automahout autonomously tracks cells in time-lapse images using a self-tuning system that annotates, trains, and refines models without human input, achieving high TRA scores on public datasets.

This study compares spindle behavior in C. elegans and C. inopinata embryos, finding differences in pronuclear migration and spindle oscillations linked to changes in cortical force generation.

Mastodon is a software platform for analyzing large-scale lineage-tracing microscopy datasets, enabling manual and automated cell tracking and lineage analysis in complex 3D geometries.

This study identifies a novel post-arrival behavior called 'leaving' in C. elegans using an immobilization-free chemotaxis assay, showing it is regulated by the egl-4 gene.

This paper develops a self-supervised model to predict aging and lifespan from behavioral data in killifish, finding that single-day predictions can match whole-life models for some traits.

The paper introduces a computational framework to extract mechanistic hypotheses from morphological dynamics data by analyzing correlations and gene perturbations in C. elegans embryos.

The paper introduces image-scanning light-sheet microscopy to enable high-speed volumetric imaging of complex biological dynamics with improved speed while maintaining resolution and efficiency.

The paper shows that inactivating the NMD pathway suppresses the embryonic lethality of gsr-1 mutants in C. elegans by enabling the transsulfuration pathway to compensate for the loss of glutathione reductase function.

The paper introduces a high-resolution volumetric imaging system for observing cellular dynamics in large 3D tissues and embryos, demonstrating its application in mouse brain and quail embryo studies.

This study shows that SMC5/6-mediated confinement of negative supercoils enables Top2A to resolve them during DNA replication, ensuring genome stability, and identifies over-accumulation of supercoils in cancer cells.

The paper creates an atlas and database of neuropeptide gene expression in the adult zebrafish forebrain, identifying novel subnuclei and comparing them to mouse hypothalamic regions.

The paper harmonizes whole-brain imaging datasets from multiple labs to enable automated neuron identification and identifies factors influencing neuron positioning in C. elegans.

The paper examines enhancer-promoter interactions in mouse embryonic stem cells, finding that transcriptional activity increases genomic viscosity, stabilizing these interactions.

This paper describes OME-Zarr, a cloud-optimized bioimaging file format developed through community collaboration to improve scalability and data access.

The paper describes a specialized microscope system for long-term live imaging of a mouse embryo, revealing new developmental phenomena.

This study systematically quantifies cell morphodynamics in C. elegans embryos, revealing high reproducibility and unique dynamics across cells.

PHi-C2 converts Hi-C data into dynamic 3D genome models using polymer modeling and provides an optimized algorithm and Colab workflow for analysis.

This study shows that the PAF1 complex is required for oogenesis in C. elegans by promoting oocyte maturation gene expression.

The paper quantifies age-related changes in C. elegans oocyte cytoplasmic texture using statistical image processing methods.

The paper creates a deep collection of quantitative nuclear division dynamics data from RNAi-treated C. elegans embryos, identifies 8660 reproducible RNAi phenotypes, and suggests 24 functional processes in early embryogenesis.

BD5 is a new HDF5-based data format for biological dynamics data that allows fast random access, improving data reuse compared to XML-based BDML.

PHi-C simulates dynamic 3D genome features from Hi-C data, aligning with live-cell imaging observations and providing physical insights.