Lydia Ng

Iterative co-creation of harmonized human and non-human primate cellular and structural ontologies and 3D common coordinate frameworks for the basal ganglia

The paper describes the iterative creation of harmonized ontologies and 3D frameworks for the basal ganglia across human and non-human primates to enable cross-species comparisons of cellular and molecular data.

A layered standards framework for integrating single-cell and spatial omics data into brain cell atlases

This paper introduces a standards framework for integrating single-cell and spatial omics data into brain cell atlases, enabling interoperable and reusable knowledge-ready resources.

MapMyCells: High-performance mapping of unlabeled cell-by-gene data to reference brain taxonomies

MapMyCells maps unlabeled single-cell datasets to reference brain taxonomies, enabling cross-study integration and reproducible cell-type annotation.

A consensus spinal cord cell type atlas across mouse, macaque, and human

The paper creates a cross-species spinal cord cell type atlas integrating data from mouse, macaque, and human, identifying conserved and species-specific features.

A curvilinear coordinate flatmap for visualizing hippocampal structure and development

This paper introduces a curvilinear coordinate flatmap method to visualize hippocampal structure and development, revealing topographic variations obscured in standard coordinate systems.

Cross-species consensus atlas of the primate basal ganglia

The paper creates a cross-species consensus atlas of primate basal ganglia cell types using multiomic data from human, macaque, and marmoset, identifying 61 conserved cell types and a novel hybrid medium spiny neuron type.

A cross-species spatial transcriptomic atlas of the human and non-human primate basal ganglia

This paper creates a cross-species spatial transcriptomic atlas of the basal ganglia in human, rhesus macaque, and common marmoset, revealing conserved molecular organization and cell type-specific compartments.

The ANTsX Ecosystem for Mapping the Mouse Brain

The paper demonstrates the use of ANTsX for precise spatial mapping of the mouse brain using standardized coordinate systems and presents novel workflows for longitudinal trajectory analysis and automated morphological measurements.

The transcriptomic and spatial organization of telencephalic GABAergic neuronal types

The paper analyzes the transcriptomic and spatial organization of GABAergic neurons in the mouse telencephalon, revealing complex developmental and spatial relationships across multiple brain regions.

Data-driven fine-grained region discovery in the mouse brain with transformers

This paper introduces CellTransformer, a self-supervised framework for detecting fine-grained spatial domains in mouse brain spatial transcriptomics data, achieving high consistency across large datasets.

Integrated Classification of Cortical Cells and Quantitative Projectomic Mapping Unveil Organizational Principles of Brain-Wide Connectomes at Single Cell Level

This study integrates molecular and morphological data to classify cortical neurons and map their connectomes, revealing organizational principles of brain-wide networks at the single-cell level.

A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types

The paper develops a toolkit of transgenic mouse lines and enhancer AAVs for selective targeting of cortical cell populations using transcriptomic and epigenomic data.

Developmental Mouse Brain Common Coordinate Framework

The paper develops a 3D developmental common coordinate framework (DevCCF) for mouse brains across multiple developmental stages to enable data integration and analysis of brain development.

Integrated multimodal cell atlas of Alzheimer's disease

This study creates an integrated multimodal cell atlas of Alzheimer's disease by analyzing single nuclei transcriptomes, epigenomes, and spatial coordinates across AD stages.

A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

This paper creates a high-resolution transcriptomic and spatial cell type atlas of the whole adult mouse brain, revealing spatial organization and transcription factor codes for cell types.

epDevAtlas: Mapping GABAergic cells and microglia in postnatal mouse brains

The paper creates high-resolution 3D atlases of postnatal mouse brains and maps changes in GABAergic cells and microglia across development.

Stimulus novelty uncovers coding diversity in survey of visual cortex

The paper identifies diverse functional neuron types in the visual cortex that process novel and familiar stimuli in mice.

A whole-brain monosynaptic input connectome to neuron classes in mouse visual cortex

The paper maps brain-wide monosynaptic inputs to specific neuron classes in mouse visual cortex using an improved rabies virus tracing strategy and identifies connectivity patterns within and between visual areas.

The BRAIN Initiative Cell Census Data Ecosystem: A User's Guide

The paper provides a guide to the BRAIN Initiative Cell Census Network (BICCN) data ecosystem, its tools, and resources for analyzing brain cell types across species.

The Neurodata Without Borders ecosystem for neurophysiological data science

The paper describes the Neurodata Without Borders (NWB) ecosystem, which enables FAIR neurophysiological data management and analysis across species and modalities.

A multimodal cell census and atlas of the mammalian primary motor cortex

The paper generates a multimodal cell census and atlas of the mammalian primary motor cortex, revealing a unified molecular genetic landscape and cross-species taxonomy of cell types.

Cellular Anatomy of the Mouse Primary Motor Cortex

The paper provides a detailed cellular-resolution map of the mouse primary motor cortex, defining cell types and their connectivity.

Cellular resolution anatomical and molecular atlases for prenatal human brains

This study creates two high-resolution anatomical atlases of prenatal human brains at PCW 15 and 21, annotated with gene expression and cytoarchitecture to identify developmental features.

A survey of spiking activity reveals a functional hierarchy of mouse corticothalamic visual areas

The paper presents a dataset and analysis of spiking activity across multiple mouse visual areas, revealing that functional connectivity mirrors anatomical hierarchy.

Regional, layer, and cell-class specific connectivity of the mouse default mode network

This study identifies the anatomical composition and connectivity patterns of the mouse default mode network at the regional, layer, and cell-class levels.

Toward an integrated classification of neuronal cell types: morphoelectric and transcriptomic characterization of individual GABAergic cortical neurons

The paper characterizes transcriptomic and physiological properties of GABAergic cortical neurons in mice, identifying 20 interneuron met-types with consistent features across modalities.

Brain-wide single neuron reconstruction reveals morphological diversity in molecularly defined striatal, thalamic, cortical and claustral neuron types

Complete morphologies of 1,708 neurons, sparsely labelled and imaged whole-brain with fMOST, expose region-specific long-range projection rules and finer diversity than current transcriptomic subtypes capture.

A large-scale, standardized physiological survey reveals higher order coding throughout the mouse visual cortex

The paper presents a large-scale dataset of neural activity in the mouse visual cortex and shows that responses to different stimuli are largely independent, suggesting multi-layer hierarchical computation.

The organization of intracortical connections by layer and cell class in the mouse brain

The paper expands the Allen Mouse Brain Connectivity Atlas by analyzing intracortical connections at the layer and cell class level, revealing modular organization and distinct projection patterns.

Conserved cell types with divergent features between human and mouse cortex

The paper compares cell types in human and mouse cortex using single nucleus RNA-sequencing, finding conserved architecture with species-specific differences.