spatial domain detection

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.

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.

Spatiotemporal mapping of endothelial proliferative response in acute chemical liver injury

This study characterizes the spatiotemporal proliferative response of endothelial cells in acute liver injury and introduces a novel pipeline for analyzing hepatic cell states.

Host specificity, seasonality, and urbanicity shape the gut microbiome of a synanthropic insect

This study examines how host plant, season, and urbanization affect the gut microbiome of soapberry bugs, finding that host plant is the primary driver of microbial community structure.

Molecule-resolved inference reveals the spatial organization of transcriptional programs

The paper introduces FICTURE2, a statistical model that infers transcriptional programs from individual RNA molecules in spatial transcriptomics data, revealing spatial organization and cellular identity without segmentation.

Spatialsnake: a flexible workflow for spatial transcriptomics analysis across platforms

Spatialsnake provides a flexible workflow for spatial transcriptomics analysis across multiple platforms, enabling analysis of selected populations and tissue regions with adjustable parameters.

Growing Macroscopic Functional Human Tissues on 3D Printed Peptide Hydrogels

This study demonstrates growing macroscopic functional human tissues on 3D-printed peptide hydrogels, enabling centimeter-scale neural organoids and directional axonal communication.

FennoTraits: Dataset of plant functional traits and community composition in northern European flora

The paper introduces FennoTraits, a dataset of plant functional traits and community composition from northern European flora, highlighting trait patterns and species distribution across seven study areas.

Cornealia: automated collective order analysis reveals density-dependent reorganization of donor corneal endothelium

Cornealia analyzes collective order in donor corneal endothelium, revealing density-dependent reorganization and mechanical responses not captured by traditional metrics.

Climate-associated genomic variation across life stages reveals population-specific signals of local adaptation in European beech

The paper identifies climate-associated genomic variation in European beech across life stages, revealing population-specific adaptive responses to temperature and precipitation changes.

Quantitative assessment of mesoscale cellular order and organization in the mouse hippocampus

The paper quantifies mesoscale cellular organization in the mouse hippocampus using a new software tool, revealing cell-type-specific nuclear shape variations and positionally ordered but orientationally disordered dense regions.

Multi-scale histology reveals localized ageing signatures in normal human colon

This paper uses multi-scale histology to identify localized age-related changes in normal human colon tissue using H&E images and machine learning.

MorphoDeep enables fast 3D cell instance segmentation by learning cell interfaces and junctions

MorphoDeep improves 3D cell segmentation by learning cell interfaces and junctions, achieving higher accuracy and speed than existing methods.

Epigenomic heterogeneity and spatial organization during human reprogramming

This study examines epigenomic and spatial changes during human reprogramming, finding distinct molecular and spatial patterns in productive versus unsuccessful trajectories.

Social Approach Dynamics in Freely-Moving Rat Dyads are Not Impacted by Lesions to the Retrosplenial Cortex

This study shows that lesions to the retrosplenial cortex in rats do not significantly affect social approach dynamics during interactions with a social stimulus.

The SWAN atlas: an open multimodal resource combining neuroimaging and high-resolution histology of the human brain in stereotactic space

The paper presents the SWAN atlas, a multimodal resource combining neuroimaging and high-resolution histology of the human brain in stereotactic space to improve localization accuracy for clinical applications.

SVC: A Vision Transformer-based Spatially and Virtually Embedded Cell Model for Deciphering Subcellular Spatial Transcriptomic Heterogeneity

SVC predicts subcellular transcript localization and co-organization using a Vision Transformer model, revealing disease patterns and spatial biology not accessible at the cell level.

Neuronal and vascular genome-maintenance states organize opposing multicellular architectures in the aging brain

The paper maps DNA damage response states in aging mouse brains, revealing opposing neuronal and vascular spatial patterns linked to genome maintenance.

The social structure of a captive group of Rüppell's vultures (Gyps rueppellii)

This study examines the social structure of captive Rüppell's vultures, revealing stable dominance hierarchies and complex social bonds influenced by breeding season and pair-bond status.

SORT disentangles multilevel gene programs across heterogeneous spatial transcriptomic atlases

SORT identifies multilevel gene programs and their spatial activities across diverse spatial transcriptomic datasets, revealing both shared and sample-specific patterns.

Absence of the Earths magnetic field activates stress-related brain circuits in a mammal

The study identifies stress-related brain circuits activated by the absence of Earth's magnetic field in mole-rats using a novel imaging pipeline.

Water Kefir as a Model for Aggregative Development of Microbial Multicellularity within a Multispecies Biofilm

This study investigates water kefir grains as a model for microbial multicellularity, revealing an emergent growth function in multispecies biofilms.

Spatially resolved transcriptomics of poplar reveals tissue organization across shoot-associated organs

This study creates a spatial transcriptome atlas of poplar shoot-associated organs, revealing tissue organization and gene expression patterns across different developmental stages and anatomical contexts.

REZCUE: Rescuing 3D spatial omics from archived FFPE tissue

REZCUE enables 3D spatial multi-omic analysis of archived FFPE tissue by preserving nucleic acids and proteins for subsequent assays.

Conserved Fibroblast Subsets Drive Shared Fibrotic Mechanisms in Osteoarthritis Synovium and Systemic Sclerosis Skin

This study identifies conserved fibroblast subsets and fibrotic mechanisms in osteoarthritis and systemic sclerosis using single-cell RNA-seq and spatial transcriptomics.

Behavioral arousal organizes visual cortical population micro-states across the sleep-wake cycle

The paper shows that visual cortical population micro-states are organized by behavioral arousal rather than discrete sleep-wake states in mice.

Optogenetic BMP4 models symmetry breaking and primitive streak formation in hPSCs

This paper introduces LightBMP, an optogenetic tool to control BMP4 in hPSCs, showing spatial BMP4 patterns can drive symmetry breaking and primitive streak formation without mechanical cues.

SFUMATO: Bayesian probabilistic clustering for uncertainty-aware spatialtranscriptomics analysis and mapping

SFUMATO provides a Bayesian probabilistic framework for spatial transcriptomics that captures uncertainty and enables continuous visualization of transcriptional domains.

Precipitation seasonality and soil carbon shape Arcellinida diversity across Bulgaria's ecosystems

This study examines Arcellinida diversity across Bulgaria's ecosystems, finding that stable humidity and intermediate soil carbon stocks enhance richness, while acidic peatlands host unique taxa.

Network Adaptability Governs Resilience and Susceptibility to Social Defeat

The paper investigates resilience and susceptibility to social defeat stress in mice using brain imaging, identifying structural and network-level differences associated with coping mechanisms.