spatial domain detection

This paper introduces f-LENNS, an AI framework that enhances fMRI resolution without retraining, improving spatial fidelity and generalizing to atypical brain function.

spSheaf infers spatial domains from raw molecular data without cell segmentation, outperforming existing methods on benchmark datasets.

SigDoTS is a statistical framework for spatial domain detection in spatial transcriptomics that controls for post-selection bias and improves domain recovery.

The paper develops a spatial proteomics workflow to study early astrocytic remodeling in an ALS mouse model, finding that motor neurons are surrounded by GFAP-high environments earlier than previously observed.

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

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

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

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

The paper identifies a pre-fibrotic stage in scleroderma by analyzing spatial transcriptomic changes in clinically uninvolved skin, showing early loss of fibroblast niches and vascular reprogramming.

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

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.

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

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.

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

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

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.

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.

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.

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

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

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

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

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

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

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

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

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.

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.

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.