spatial domain detection

THiRST: Computer Vision Empowered Three-dimensional High-Resolution Spatial Transcriptomics Analytics

THiRST reconstructs 3D spatial transcriptomic data from serial 2D sections, improving cross-section consistency and enabling 3D gene expression analysis.

MorphoANOVA: Dissecting Histology-Gene Expression Relationships in Spatial Transcriptomics

MorphoANOVA systematically analyzes spatial gene-expression patterns in relation to tissue morphology, identifying genes with location-specific associations and spatial expression beyond morphology.

Microenvironmental Fingerprint of Maturing Tau Condensates from Spectral and Lifetime Phasor Analysis of a Solvatochromic Dye

This paper develops a multimodal framework using spectral and lifetime phasor analysis to characterize microenvironmental changes in Tau condensates during maturation.

Three-dimensional mapping of human lung fibrosis identifies spatial coupling between tissue microarchitecture and maladaptive repair states

This study maps human lung fibrosis in 3D, showing how structural changes in tissue microarchitecture drive maladaptive repair states and disease progression.

Homeostatic fibroblast niche collapse in clinically uninvolved skin marks a pre-fibrotic stage of systemic sclerosis

The paper identifies a pre-fibrotic stage in scleroderma by analyzing spatial transcriptomic changes in clinically uninvolved skin, showing early reprogramming of fibroblasts and vascular smooth muscle cells.

A biological light sheet links cellular voltage to mesoscopic brain dynamics

This paper introduces SPress, a method that enables high-speed, high-contrast voltage imaging of large neuronal populations in vivo with mesoscopic resolution.

A single-cell transcriptomic atlas of paper wasp brains highlights Kenyon cells' role in social behavior

The paper uses single-cell transcriptomics to analyze brain cells in paper wasps, showing that Kenyon cells vary with social roles and respond to social interactions.

Generative 3D Spatial Reconstruction of Cellular Organization from Single Cell Expression

ORBIS reconstructs 3D tissue geometry from single-cell gene expression without spatial references, achieving lower shape error and faster sampling than existing methods.

Measuring neuronal input-output operations in vivo with random access projection microscopy

This paper introduces SLAP2, a high-speed microscope for measuring submicron synapses and dendritic voltage in behaving mice, revealing nonlinear input-output amplification in neurons.

Persistent hippocampal traces of lifelong spatial memory

The paper shows that mice retain spatial memory in the hippocampus after long absences, with neural patterns persisting despite changes in individual neuron activity.

Midlife nonlinearities across scale in Biondi body amyloid formation in the human choroid plexus

The paper examines age-related accumulation of Biondi bodies in human choroid plexus epithelial cells, finding nonlinear increases in prevalence and load, and suggesting prion-like spread mechanisms.

MorphoProt: RNA-Conditioned Integration of Multiscale Histology for Spatial Protein Inference

MorphoProt predicts spatial protein abundance using RNA expression, multiscale histology, and tissue neighborhoods, outperforming baselines in human and mouse tissues.

Deep Recovery of Effective Migration Surfaces

This paper introduces dreems, a graph neural network that efficiently estimates effective migration surfaces from genetic data, achieving lower error and faster computation than existing methods.

Organ scale Three-dimensional atlas of developing pelvic innervation for the mouse lower urinary tract.

The paper creates a 3D atlas of pelvic innervation development in mice, revealing migration patterns, neurogenesis timing, and structural changes in pelvic ganglia across developmental stages.

Single-probe, high-yield spatial mapping of diverse short RNA motifs

The paper introduces SMOOTHY-FISH, a method to visualize short RNA motifs at single-molecule resolution, revealing new spatial RNA biology insights in single cells and mouse brain tissues.

Generalizable virtual staining from histopathology to spatial proteomics across biological scales

This study introduces QUEST, a model that uses H&E histology to predict spatial protein expression, enabling virtual staining and analysis across biological scales.

Gene expression in Anolis sagrei suggests conservation of patterning mechanisms drives formation of two high acuity areas

The paper identifies conserved gene expression patterns in the retina of Anolis sagrei that suggest shared developmental mechanisms for forming multiple high acuity areas.

Topographic reference modelling of white matter hyperintensities across the adult lifespan

This paper introduces vTRM, a framework to characterize WMH spatial patterns across age and sex, revealing distinct associations with aging, vascular, and neurodegenerative processes.

Distinct processing of visual motion by transcriptomic cell types in the superior colliculus

The paper identifies how three transcriptomic cell types in the superior colliculus process visual motion with distinct feature selectivity, morphology, and connectivity.

Spatial transcriptomics of pediatric tuberculosis lymph nodes reveals a conserved hypoxia_SPP1 niche

This study uses spatial transcriptomics to identify a hypoxia-associated SPP1-enriched microenvironment in pediatric TB granulomas that may contribute to incomplete bacterial clearance.

Predicting cortical signal mixing in coarse-resolution fMRI: a forward-operator analysis of surface mapping and the conditional benefit of correction

This paper develops a forward-operator model to predict signal mixing in fMRI and shows that correcting for it improves coarse-resolution cortical mapping.

Pain Matters: Nociceptive signaling drives neural encoding of inflammatory responses

The paper shows that nociceptive signaling is essential for the brain to represent and replay inflammatory states using human fMRI and mouse activity mapping.

Why probe registration is crucial for infant fNIRS and HD-DOT? An evaluation across 49 newborns

This study evaluates probe registration accuracy in newborn fNIRS and HD-DOT, showing significant cap misalignment affecting spatial accuracy of functional images.

Quantum Dot-Based Non-invasive Monitoring of Sinusoidal Endothelial Scavenger Function in Steatohepatitis

This study develops a non-invasive method using quantum dots to assess liver sinusoidal endothelial cell scavenger function in MASH, showing reduced retention correlates with disease progression.

Dog and Human Brains Represent Human Emotional Bodies with Asymmetric Encoding of Happiness and Anger

This study shows that dogs and humans have similar neural representations of human bodily emotions, with happiness and anger encoded asymmetrically in distinct brain regions.

Light-sheet fluorescence microscopy of optically cleared human head-and-neck organs: three-dimensional tissue assessment and histological correlation

This study uses optical clearing and light-sheet fluorescence microscopy to visualize 3D microanatomy of human head-and-neck tissues and correlate it with conventional histology.

Brain-wide representations of olfactory behavior in C. elegans

The paper analyzes brain-wide neural activity in C. elegans during olfactory navigation and identifies functional circuits linking sensory input to motor behavior across different environments and behavioral states.

WhaleSonic: Recordings of cetacean vocal behaviour with hydrophone arrays in Northern Norway

WhaleSonic provides a raw acoustic dataset of cetacean vocalizations in Northern Norway, supporting multichannel algorithms for source separation and communication analysis.

TileScope quantifies spatial gene expression relationships beyond colocalization

TileScope quantifies spatial gene expression relationships beyond simple colocalization, distinguishing regional enrichment from internal covariation in glioblastoma and other tissues.

Cross-species structure-mechanics prediction in the intervertebral disc

This study develops a cross-species framework linking collagen structure to mechanical vulnerability in intervertebral discs using multiscale imaging and modeling.