Jack Waters

Robust and accessible in situ sequencing with an open-source automated sequencer

The paper introduces Seq-o-Matic, an open-source automated in situ sequencer that reduces hands-on time and improves sequencing consistency across tissue sections.

3D-MAESTRO: A scalable, modular, portable pipeline for automated processing of large-scale volumetric brain microscopy data

3D-MAESTRO automates processing of large-scale volumetric brain microscopy data, enabling scalable and reproducible analysis of mouse brain structures.

Multiregional single-cell profiling reveals shared and specialized cellular vulnerability in Alzheimer's disease

This study uses single-nucleus RNA-seq, ATAC-seq, and Multiome to analyze Alzheimer's disease across multiple brain regions, revealing shared and region-specific cellular vulnerabilities.

Multimodal characterization of variation in neuronal types in the mouse basal ganglia

This study uses multimodal Patch-seq data to show that gene expression gradients in mouse basal ganglia neurons correlate with spatial location, physiology, and morphology.

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 Cross-Species Enhancer-AAV Toolkit for Cell Type-Specific Targeting Across the Basal Ganglia

The paper develops a cross-species enhancer-AAV toolkit for targeting specific cell types in the basal ganglia across species, validated in mouse and macaque.

Morphoelectric Diversity and Specialization of Neuronal Cell Types in the Primate Striatum

The paper analyzes multi-modal Patch-seq data from macaque striatum to reveal morphoelectric diversity and functional specialization of neuronal cell types, highlighting primate-specific features and differences from rodents.

SCALPEL: A pipeline for processing large-scale spatial transcriptomics data

SCALPEL processes large-scale spatial transcriptomics data with improved 3D segmentation, doublet detection, and spatial alignment, showing better performance than previous methods.

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.

The Caudate Nucleus Exhibits Distinct Pathology and Cell Type-Specific Responses Across Alzheimer's Disease

The paper maps AD-related pathological changes in the caudate nucleus at cellular resolution, identifying distinct features and cell type-specific responses.

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.

Spatial patterning of transcriptional and regulatory programs in the primate subcortex

The paper presents a spatially resolved transcriptomic and gene regulatory atlas of primate subcortical regions, revealing spatially tuned transcriptional and regulatory programs across cell types.

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.

Exploring the correspondence between gene expressionand thalamic nuclei using the THALMANAC resource

The paper introduces THALMANAC, a resource for analyzing single-cell transcriptomic data of the thalamus, revealing gene expression patterns that support and refine thalamic nucleus parcellation.

Hebb's Vision: The Structural Underpinnings of Hebbian Assemblies

The paper identifies neural assemblies consistent with Hebb's theory using a novel dataset linking optical physiology to connectivity, finding they are structurally integrated but not defined by strong monosynaptic connections.

MerQuaCo: a computational tool for quality control in image-based spatial transcriptomics

The paper introduces MerQuaCo, an open-source tool to automatically detect and quantify imperfections in spatial transcriptomics data, improving quality assessment.

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.

Impaired capillary-venous drainage contributes to gliosis and demyelination in white matter during aging

The paper shows that impaired capillary-venous drainage in aging mice leads to hypoperfusion, gliosis, and demyelination in deep white matter regions.

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.

Microscale visualization of cellular features in adult macaque visual cortex

The paper visualizes dense distributions of immunolabeled proteins in adult macaque visual cortex using expansion microscopy and light sheet imaging, enabling multimodal atlas creation.

Morpho-electric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex

The paper identifies transcriptomic and morpho-electric diversity in human neocortical layer 1 interneurons, revealing greater subclass distinction compared to mouse.

Signature morpho-electric properties of diverse GABAergic interneurons in the human neocortex

The paper uses viral labeling and Patch-seq to define morpho-electric properties of GABAergic interneurons in human neocortex, revealing functional insights and reclassifying some SST neurons into PVALB subclass.

Enhancer-AAVs allow genetic access to oligodendrocytes and diverse populations of astrocytes across species

The paper develops AAV-based genetic tools to specifically target astrocytes and oligodendrocytes across species, revealing functional roles in reward-dependent acetylcholine responses.

Motion/direction-sensitive thalamic neurons project extensively to the middle layers of primary visual cortex

The paper shows motion/direction-sensitive thalamic neurons project more to middle layers of V1 than previously thought, challenging existing views on thalamocortical organization.

Relationship between simultaneously recorded spiking activity and fluorescence signal in GCaMP6 transgenic mice

The paper characterizes the relationship between spiking activity and fluorescence signals in GCaMP6-expressing neurons, finding GCaMP6s has better single-spike detection than GCaMP6f.

The effect of inclusion criteria on the functional properties reported in mouse visual cortex

This study shows how different inclusion criteria in calcium imaging affect reported tuning properties of mouse visual cortex neurons, leading to conflicting results between studies.

Superficial bound of the depth limit of 2-photon imaging in mouse brain

The paper determines the depth limit of 2-photon imaging in mouse brain tissue by comparing 2- and 3-photon excitation, finding accuracy ceases at 450 m where in- and out-of-focus fluorescence balance.

The spatial structure of feedforward information in mouse primary visual cortex

The paper maps the functional and structural properties of feedforward projections from the LGN to V1 in mice, revealing differences in receptive fields and depth-dependent biases between location-sensitive and motion-sensitive axons.

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.

Separation of hemodynamic signals from GCaMP fluorescence measured with widefield imaging

The paper develops a spatially-detailed regression model to separate hemodynamic signals from GCaMP fluorescence in widefield imaging of awake mice, improving accuracy near blood vessels and along the sagittal midline.