Segmenting individual instances of mitochondria from imaging datasets can provide rich quantitative information, but is prohibitively time-consuming when done manually, prompting interest in the development of automated algorithms using deep neural networks. Existing solutions for various segmentation tasks are optimized for either: high-resolution three-dimensional imaging, relying on well-defined object boundaries (e.g., whole neuron segmentation in volumetric electron microscopy datasets); or low-resolution two-dimensional imaging, boundary-invariant but poorly suited to large 3D objects (e.g., whole-cell segmentation of light microscopy images). Mitochondria in whole-cell 3D electron microscopy datasets often lie in the middle ground - large, yet with ambiguous borders, challenging current segmentation tools. To address this, we developed skeleton-oriented object segmentation (SKOOTS) - a novel approach that efficiently segments large, densely packed mitochondria. SKOOTS accurately and efficiently segments mitochondria in previously difficult contexts and can also be applied to segment other objects in 3D light microscopy datasets. This approach bridges a critical gap between existing segmentation approaches, improving the utility of automated analysis of three-dimensional biomedical imaging data. We demonstrate the utility of SKOOTS by applying it to segment over 15,000 cochlear hair cell mitochondria across experimental conditions in under 2 hours on a consumer-grade PC, enabling downstream morphological analysis that revealed subtle structural changes following aminoglycoside exposure - differences not detectable using analysis approaches currently used in the field.

Stress is a natural response of the body to perceived threats, and it can have both positive and negative effects on brain hemodynamics. Stress-induced changes in pupil and eyelid size/shape have been used as a biomarker in several fMRI studies. However, there were limited knowledges regarding changes in behavior of pupil and eyelid dynamics, particularly on animal models. In the present study, the pupil and eyelid dynamics were carefully investigated and characterized in a newly developed awake rodent fMRI protocol. Leveraging deep learning techniques, the mouse pupil and eyelid diameters were extracted and analyzed during different training and imaging phases in the present project. Our findings demonstrate a consistent downwards trend in pupil and eyelid dynamics under a meticulously designed training protocol, suggesting that the behaviors of the pupil and eyelid can be served as reliable indicators of stress levels and motion artifacts in awake fMRI studies. The current recording platform not only enables the facilitation of awake animal MRI studies but also highlights its potential applications to numerous other research areas, owing to the non-invasive nature and straightforward implementation.

Magnetic resonance imaging (MRI) is commonly used in healthcare for its ability to generate diverse tissue contrasts without ionizing radiation. However, this flexibility complicates downstream analysis, as computational tools are often tailored to specific types of MRI and lack generalizability across the full spectrum of scans used in healthcare. Here, we introduce a versatile framework for the development and validation of AI models that can robustly process and analyze the full spectrum of scans achievable with MRI, enabling model deployment across scanner models, scan sequences, and age groups. Core to our framework is UltimateSynth, a technology that combines tissue physiology and MR physics in synthesizing realistic images across a comprehensive range of meaningful contrasts. This pan-contrast capability bolsters the AI development life cycle through efficient data labeling, generalizable model training, and thorough performance benchmarking. We showcase the effectiveness of UltimateSynth by training an off-the-shelf U-Net to generalize anatomical segmentation across any MR contrast. The U-Net yields highly robust tissue volume estimates, with variability under 4% across 150,000 unique-contrast images, 3.8% across 2,000+ low-field 0.3T scans, and 3.5% across 8,000+ images spanning the human lifespan from ages 0 to 100.

The construction of growth charts trained to predict age or developmental deviation (the brain-age index) based on structural/functional properties of the brain may be informative of childrens neurodevelopmental trajectories. When applied to both typically and atypically developing populations, results may indicate that a particular condition is associated with atypical maturation of certain brain networks. Here, we focus on the relationship between reading disorder (RD) and maturation of functional connectivity (FC) patterns in the prototypical reading/language network using a cross-sectional sample of N = 742 participants aged 6-21 years. A support vector regression model is trained to predict chronological age from FC data derived from a whole-brain model as well as multiple reduced models, which are trained on FC data generated from a successively smaller number of regions in the brains reading network. We hypothesized that the trained models would show systematic underestimation of brain network maturity for poor readers, particularly for the models trained with reading/language regions. Comparisons of the different models predictions revealed that while the whole-brain model outperforms the others in terms of overall prediction accuracy, all models successfully predicted brain maturity, including the one trained with the smallest amount of FC data. In addition, all models showed that reading ability affected the brain-age gap, with poor readers ages being underestimated and advanced readers ages being overestimated. Exploratory results demonstrated that the most important regions and connections for prediction were derived from the default mode and frontoparietal control networks. GlossaryDevelopmental dyslexia / reading disorder (RD): A specific learning disorder affecting reading ability in the absence of any other explanatory condition such as intellectual disability or visual impairment Support vector regression (SVR): A supervised machine learning technique which predicts continuous outcomes (such as chronological age) rather than classifying each observation; finds the best-fit function within a defined error margin Principal component analysis (PCA): A dimensionality reduction technique that transforms a high-dimensional dataset with many features per observation into a reduced set of principal components for each observation; each component is a linear combination of several original (correlated) features, and the final set of components are all orthogonal (uncorrelated) to one another Brain-age index: A numerical index quantifying deviation from the brains typical developmental trajectory for a single individual; may be based on a variety of morphometric or functional properties of the brain, resulting in different estimates for the same participant depending on the imaging modality used Brain-age gap (BAG): The difference, given in units of time, between a participants true chronological age and a predictive models estimated age for that participant based on brain data (Actual - Predicted); may be used as a brain-age index HighlightsO_LIA machine learning model trained on functional data predicted participants ages C_LIO_LIThe model showed variability in age prediction accuracy based on reading skills C_LIO_LIThe model highly weighted data from frontoparietal and default mode regions C_LIO_LINeural markers of reading and language are diffusely represented in the brain C_LI

Sepsis is an abnormally dysregulated immune response against infection in which the human immune system ranges from a hyper-inflammatory phase to an immune-suppressive phase. Current assessment methods are limiting owing to time-consuming and laborious sample preparation protocols. We propose a rapid label-free imaging-based technique to assess the immune status of individual human monocytes. High-resolution intracellular compositions of individual monocytes are quantitatively measured in terms of the three-dimensional distribution of refractive index values using holotomography, which are then analyzed using machine-learning algorithms to train for the classification into three distinct immune states: normal, hyper-inflammation, and immune suppression. The immune status prediction accuracy of the machine-learning holotomography classifier was 83.7% and 99.9% for one and six cell measurements, respectively. Our results suggested that this technique can provide a rapid deterministic method for the real-time evaluation of the immune status of an individual.

Mitochondrial morphology and structural changes are closely associated with metabolic dysfunction and disease progression. However, the structural complexity of mitochondria presents a major challenge for accurate segmentation and analysis. Most existing methods focus on delineating entire mitochondria but lack the capability to resolve fine internal features, particularly cristae. In this study, we introduce MitoStructSeg, a deep learning-based framework for mitochondrial structure segmentation and quantitative analysis. The core of MitoStructSeg is AMM-Seg, a novel model that integrates domain adaptation to improve cross-sample generalization, dual-channel feature fusion to enhance structural detail extraction, and continuity learning to preserve spatial coherence. This architecture enables accurate segmentation of both mitochondrial membranes and intricately folded cristae. MitoStructSeg further incorporates a quantitative analysis module that extracts key morphological metrics, including surface area, volume, and cristae density, allowing comprehensive and scalable assessment of mitochondrial morphology. The effectiveness of our approach has been validated on both human myocardial tissue and mouse kidney tissue, demonstrating its robustness in accurately segmenting mitochondria with diverse morphologies. In addition, we provide an open source, user-friendly tool to ensure practical usability.

The brain exhibits rich oscillatory dynamics that play critical roles in vigilance and cognition, such as the neural rhythms that define sleep. These rhythms continuously fluctuate, signaling major changes in vigilance, but the widespread brain dynamics underlying these oscillations are difficult to investigate. Using simultaneous EEG and fast fMRI in humans who fell asleep inside the scanner, we developed a machine learning approach to investigate which fMRI regions and networks predict fluctuations in neural rhythms. We demonstrated that the rise and fall of alpha (8-12 Hz) and delta (1-4 Hz) power, two canonical EEG bands critically involved with cognition and vigilance, can be predicted from fMRI data in subjects that were not present in the training set. This approach also identified predictive information in individual brain regions across the cortex and subcortex. Finally, we developed an approach to identify shared and unique predictive information, and found that information about alpha rhythms was highly separable in two networks linked to arousal and visual systems. Conversely, delta rhythms were diffusely represented on a large spatial scale primarily across the cortex. These results demonstrate that EEG rhythms can be predicted from fMRI data, identify large-scale network patterns that underlie alpha and delta rhythms, and establish a novel framework for investigating multimodal brain dynamics.

Mental processing delineates the functions of human mind encompassing a wide range of motor, sensory, emotional, and cognitive processes, each of which is underlain by the neuroanatomical substrates. Identifying accurate representation of functional neuroanatomy substrates of mental processing could inform understanding of its neural mechanism. The challenge is that it is unclear whether a specific mental process possesses a 'functional neuroanatomy fingerprint', i.e., a unique and reliable pattern of functional neuroanatomy that underlies the mental process. To address this question, we utilized a multi-task deep learning model to disentangle the functional neuroanatomy fingerprint of seven different and representative mental processes including Emotion, Gambling, Language, Motor, Relational, Social, and Working Memory. Results based on the functional magnetic resonance imaging data of two independent cohorts of 1235 subjects from the US and China consistently show that each of the seven mental processes possessed a functional neuroanatomy fingerprint, which is represented by a unique set of functional activity weights of whole-brain regions characterizing the degree of each region involved in the mental process. The functional neuroanatomy fingerprint of a specific mental process exhibits high discrimination ability (93% classification accuracy and AUC of 0.99) with those of the other mental processes, and is robust across different datasets and using different brain atlases. This study provides a solid functional neuroanatomy foundation for investigating the neural mechanism of mental processing.

Despite the importance of memories in everyday life and the progress made in understanding how they are encoded and retrieved, the neural processes by which declarative memories are maintained or forgotten remain elusive. Part of the problem is that it is empirically difficult to measure the rate at which memories fade, even between repeated presentations of the source of the memory. Without such a ground-truth measure, it is hard to identify the corresponding neural correlates. This study addresses this problem by comparing individual patterns of functional connectivity against behavioral differences in forgetting speed derived from computational phenotyping. Specifically, the individual-specific values of the speed of forgetting in long-term memory (LTM) were estimated for 33 participants using a formal model fit to accuracy and response time data from an adaptive paired-associate learning task. Individual speeds of forgetting were then used to examine participant-specific patterns of resting-state fMRI connectivity, using machine learning techniques to identify the most predictive and generalizable features. Our results show that individual speeds of forgetting are associated with resting-state connectivity within the default mode network (DMN) as well as between the DMN and cortical sensory areas. Cross-validation showed that individual speeds of forgetting were predicted with high accuracy (r = .78) from these connectivity patterns alone. These results support the view that DMN activity and the associated sensory regions are actively involved in maintaining memories and preventing their decline, a view that can be seen as evidence for the hypothesis that forgetting is a result of storage degradation, rather than of retrieval failure.

Tissue biology involves an intricate balance between cell-intrinsic processes and interactions between cells organized in specific spatial patterns, which can be respectively captured by single cell profiling methods, such as single cell RNA-seq (scRNA-seq) and spatial transcriptomics, and histology imaging data, such as Hematoxylin-and-Eosin (H&E) stains. While single cell profiles provide rich molecular information, they can be challenging to collect routinely in the clinic and either lack spatial resolution or high gene throughput. Conversely, histological H&E assays have been a cornerstone of tissue pathology for decades, but do not directly report on molecular details, although the observed structure they capture arises from molecules and cells. Here, we leverage vision transformers and adversarial deep learning to develop the Single Cell omics from Histology Analysis Framework (SCHAF), which generates a tissue sample's spatially-resolved whole transcriptome single cell omics dataset from its H&E histology image. We demonstrate SCHAF on a variety of tissues--including lung cancer, metastatic breast cancer, placentae, and whole mouse pups--training with matched samples analyzed by sc/snRNA-seq, H&E staining, and, when available, spatial transcriptomics. SCHAF generated appropriate single cell profiles from histology images in test data, related them spatially, and compared well to ground-truth scRNA-Seq, expert pathologist annotations, or direct spatial transcriptomic measurements, with some limitations. SCHAF opens the way to next-generation H&E analyses and an integrated understanding of cell and tissue biology in health and disease.