dimensionality reduction

Intrinsic timescale develops hierarchically from sensorimotor to association cortex in youth and stabilizes in adulthood

Resting-state fMRI intrinsic timescale lengthens with age in association, not sensorimotor, cortex during ages 8-22, following the sensorimotor-association axis in two cohorts; it is largely age-stable in young adults.

AC-Diff: Anatomy-Contrast Disentangled Diffusion for Multi-Vendor Liver MRI Harmonization

AC-Diff improves liver MRI harmonization by separating anatomy from contrast, achieving better segmentation results.

SkeleSketch: An Open-Source Tool for Quantifying Microglial Morphology in Fiji/ImageJ

SkeleSketch is an open-source Fiji/ImageJ plugin that automates microglial skeletonization and morphological quantification, showing accuracy across labeling strategies and correlation with commercial software.

SpaReg: sparsity-based 3D reconstruction of tissue microenvironments at native resolution across morphological and spatial molecular modalities

SpaReg reconstructs 3D tissue microenvironments from histology, spatial proteomics, and spatial transcriptomics data, preserving morphology and enabling accurate classification and disease modeling.

Deep Representation Learning on Whole-Brain Population Dynamics Uncovers Geometrically Separable Neural Codes

The paper develops a deep-learning framework to learn interpretable representations of whole-brain neural dynamics in Drosophila without neuronal identification, revealing factorized organization along metabolic state, sensory modality, and stimulus valence axes.

Sensing the heart, seeing the world: Neural mechanisms of attentional allocation between interoception and exteroception

This study uses fMRI to compare neural networks for interoceptive and exteroceptive attention, finding distinct but interacting systems for internal and external sensory processing.

Decoding natural scenes from patterned optogenetic responses in mouse visual cortex

This paper decodes natural scenes from optogenetic responses in mouse visual cortex and shows that patterned stimulation can reproduce visual representations with high fidelity.

Minkowski Tensors as a Lightweight and Interpretable Representation for Three-Dimensional Morphology

This paper introduces Minkowski Tensors as interpretable 3D shape descriptors, showing competitive performance on biomedical image classification tasks.

Biologically grounded cell profiling across microscopy modalities

The paper introduces MorphAgent, a biologically grounded AI framework for cell profiling across microscopy modalities, improving feature design and performance in drug screening and disease analysis.

Trustworthy super-resolution reconstruction across spatial omics modalities

This paper introduces spEnhance, a computational framework that improves spatial resolution and reliability of spot-level spatial omics data across multiple modalities.

Luxar: Gaussian splatting for microscopy and scalable interactive web visualisation of multidimensional scientific data

Luxar compresses volumetric microscopy data into compact archives for interactive web visualization without requiring specialized software.

RNabel-A Standalone Software Tool for Annotating Tandem Mass Spectra of Modified Ribonucleic Acids

RNabel is a software tool for annotating tandem mass spectra of modified RNAs, supporting various modifications and formats, and providing quality metrics for spectral analysis.

Different hippocampal subfield volumes predict source memory performance and general cognitive ability in an adult lifespan sample

The paper examines associations between hippocampal subfield volumes and cognitive performance in adults across the lifespan, finding subfield-specific links to memory and non-mnemonic cognition that are age-invariant.

Optimizing an Automated Processing Pipeline for Regional Macromolecular Proton Fraction and Volume Measurements in the Brain

The paper evaluates FreeSurfer parcellation workflows using MPF maps versus MPRAGE images to assess reliability and repeatability of regional MPF and volume estimates in the brain.

Autoencoders for unsupervised analysis of rat myeloarchitecture

This study uses unsupervised deep learning to analyze rat brain histology, revealing tissue organization and detecting pathological changes without manual annotations.

SubCortexMesh: A Python toolbox for surface-based analysis of subcortical brain regions

SubCortexMesh provides a Python toolbox for surface-based analysis of subcortical brain regions, enabling automated surface estimation and shape-related metrics computation.

An automated machine vision-based index for Rett Syndrome provides a generalizable framework for modeling rare disease therapeutics

This paper develops an automated machine vision-based index for Rett Syndrome that improves preclinical phenotyping by detecting disease-relevant behaviors and reducing animal use.

Brain age prediction from structural and functional connectivity across the lifespan using connectome-based predictive modeling

This study uses connectome-based predictive modeling to predict chronological age from structural and functional brain connectivity across different lifespan stages and finds that both modalities contribute complementary age-related information.

MetaCarto: biologically faithful automatic layout for genome-scale metabolic maps

MetaCarto automatically generates readable genome-scale metabolic maps by organizing reactions into biologically meaningful layouts, matching curated pathway representations and producing 2621 maps for 108 BiGG models.

Multidimensional semantic representations emerge from multi-frequency representational similarity learning

The paper uses representational similarity learning to show that multidimensional semantic information is encoded across multiple frequencies in human ventral anterior temporal lobe.

Self-supervised Internal Learning Enhances Isotropic Resolution for Three-dimensional Fluorescence Microscopy

This paper introduces DeepIso, a self-supervised framework that enhances isotropic resolution in 3D fluorescence microscopy by restoring axial frequency content without requiring explicit PSF models or system calibration.

Voxel-Matching NORDIC: Non-local patch formation by time-series similarity increases tSNR in high-resolution BOLD fMRI

The paper introduces VM-NORDIC, a denoising method for submillimeter BOLD fMRI that improves tSNR and spatial smoothness by using non-local voxel matching.

Age-related difference in gray matter volumes is heterogeneous across cerebellar regions but neither related to the topological organization nor the associated sensorimotor function

The paper examines age-related changes in cerebellar gray matter volume across different regions and finds heterogeneous decline with no significant relationship to topological organization or sensorimotor function.

Speciesformer learns conserved cellular states for cross-species generative virtual cell modeling

Speciesformer learns conserved cellular states across species to enable cross-species generative modeling of virtual cell states and their responses to interventions.

A Computational Pipeline for Retinal Capillary Blood Flow Measurement using Adaptive Optics Line Confocal Ophthalmoscopy

This paper presents a computational pipeline for measuring retinal capillary blood flow using adaptive optics line confocal ophthalmoscopy, achieving accurate velocity measurements and improved motion correction.

msaGUI: Multispectral Analysis Graphical User Interface for Ratiometric Analysis and Background Correction

msaGUI is a no-code tool for analyzing and visualizing multispectral images through customizable workflows and exportable outputs.

Dimensional and Categorical Predictors of Theory of Mind Network Activation: A transdiagnostic fMRI Study in Psychiatric Inpatients

This study uses fMRI to examine Theory of Mind network activation in psychiatric inpatients and healthy controls, finding that dimensional symptom measures better predict brain activation than categorical diagnoses.

Semi-Automated CellProfiler Pipelines for Robust Quantification of Microglial Density, Distribution and Morphology

This paper introduces a semi-automated CellProfiler framework for quantifying microglial density, distribution, and morphology, improving accuracy over fully automated or manual methods.

mc-ASTRA maps population-level variation to interpretable multicellular tissue organization processes

mc-ASTRA integrates molecular, spatial, and sample-level data to create interpretable maps of tissue-state variability and multicellular processes.

MINT infers the latent single-cell spatial transcriptome from paired histology

MINT infers cell-resolved spatial transcriptomes from paired histology and Slide-tags data, improving alignment and expression recovery in lung adenocarcinoma.