Cellular data extraction from multiplexed brain imaging data using self-supervised Dual-loss Adaptive Masked Autoencoder.

Reliable large-scale cell detection and segmentation is the fundamental first step to understanding biological processes in the brain. The ability to phenotype cells at scale can accelerate preclinical drug evaluation and system-level brain histology studies. The impressive advances in deep learning offer a practical solution to cell image detection and segmentation. Unfortunately, categorizing cells and delineating their boundaries for training deep networks is an expensive process that requires skilled biologists. This paper presents a novel self-supervised Dual-Loss Adaptive Masked Autoencoder (DAMA) for learning rich features from multiplexed immunofluorescence brain images. DAMA's objective function minimizes the conditional entropy in pixel-level reconstruction and feature-level regression. Unlike existing self-supervised learning methods based on a random image masking strategy, DAMA employs a novel adaptive mask sampling strategy to maximize mutual information and effectively learn brain cell data. To the best of our knowledge, this is the first effort to develop a self-supervised learning method for multiplexed immunofluorescence brain images. Our extensive experiments demonstrate that DAMA features enable superior cell detection, segmentation, and classification performance without requiring many annotations. In addition, to examine the generalizability of DAMA, we also experimented on TissueNet, a multiplexed imaging dataset comprised of two-channel fluorescence images from six distinct tissue types, captured using six different imaging platforms. Our code is publicly available at https://github.com/hula-ai/DAMA.

Visual Prompting Based Incremental Learning for Semantic Segmentation of Multiplex Immuno-Flourescence Microscopy Imagery.

Deep learning approaches are state-of-the-art for semantic segmentation of medical images, but unlike many deep learning applications, medical segmentation is characterized by small amounts of annotated training data. Thus, while mainstream deep learning approaches focus on performance in domains with large training sets, researchers in the medical imaging field must apply new methods in creative ways to meet the more constrained requirements of medical datasets. We propose a framework for incrementally fine-tuning a multi-class segmentation of a high-resolution multiplex (multi-channel) immuno-flourescence image of a rat brain section, using a minimal amount of labelling from a human expert. Our framework begins with a modified Swin-UNet architecture that treats each biomarker in the multiplex image separately and learns an initial "global" segmentation (pre-training). This is followed by incremental learning and refinement of each class using a very limited amount of additional labeled data provided by a human expert for each region and its surroundings. This incremental learning utilizes the multi-class weights as an initialization and uses the additional labels to steer the network and optimize it for each region in the image. In this way, an expert can identify errors in the multi-class segmentation and rapidly correct them by supplying the model with additional annotations hand-picked from the region. In addition to increasing the speed of annotation and reducing the amount of labelling, we show that our proposed method outperforms a traditional multi-class segmentation by a large margin.

Automated detection of apoptotic bodies and cells in label-free time-lapse high-throughput video microscopy using deep convolutional neural networks.

MOTIVATION: Reliable label-free methods are needed for detecting and profiling apoptotic events in time-lapse cell-cell interaction assays. Prior studies relied on fluorescent markers of apoptosis, e.g. Annexin-V, that provide an inconsistent and late indication of apoptotic onset for human melanoma cells. Our motivation is to improve the detection of apoptosis by directly detecting apoptotic bodies in a label-free manner. RESULTS: Our trained ResNet50 network identified nanowells containing apoptotic bodies with 92% accuracy and predicted the onset of apoptosis with an error of one frame (5 min/frame). Our apoptotic body segmentation yielded an IoU accuracy of 75%, allowing associative identification of apoptotic cells. Our method detected apoptosis events, 70% of which were not detected by Annexin-V staining. AVAILABILITY AND IMPLEMENTATION: Open-source code and sample data provided at https://github.com/kwu14victor/ApoBDproject.

BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets.

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

Visual Prompting based Incremental Learning for Semantic Segmentation of Multiplex Immuno-Flourescence Microscopy Imagery.

Deep learning approaches are state-of-the-art for semantic segmentation of medical images, but unlike many deep learning applications, medical segmentation is characterized by small amounts of annotated training data. Thus, while mainstream deep learning approaches focus on performance in domains with large training sets, researchers in the medical imaging field must apply new methods in creative ways to meet the more constrained requirements of medical datasets. We propose a framework for incrementally fine-tuning a multi-class segmentation of a high-resolution multiplex (multi-channel) immuno-flourescence image of a rat brain section, using a minimal amount of labelling from a human expert. Our framework begins with a modified Swin-UNet architecture that treats each biomarker in the multiplex image separately and learns an initial "global" segmentation (pre-training). This is followed by incremental learning and refinement of each class using a very limited amount of additional labeled data provided by a human expert for each region and its surroundings. This incremental learning utilizes the multi-class weights as an initialization and uses the additional labels to steer the network and optimize it for each region in the image. In this way, an expert can identify errors in the multi-class segmentation and rapidly correct them by supplying the model with additional annotations hand-picked from the region. In addition to increasing the speed of annotation and reducing the amount of labelling, we show that our proposed method outperforms a traditional multi-class segmentation by a large margin.

Impaired Experience-Dependent Refinement of Place Cells in a Rat Model of Alzheimer's Disease.

BACKGROUND: Hippocampal place cells play an integral role in generating spatial maps. Impaired spatial memory is a characteristic pathology of Alzheimer's disease (AD), yet it remains unclear how AD influences the properties of hippocampal place cells. OBJECTIVE: To record electrophysiological activity in hippocampal CA1 neurons in freely-moving 18-month-old male TgF344-AD and age-matched wild-type (WT) littermates to examine place cell properties. METHODS: We implanted 32-channel electrode arrays into the CA1 subfield of 18-month-old male WT and TgF344-AD (n = 6/group) rats. Ten days after implantation, single unit activity in an open field arena was recorded across days. The spatial information content, in-field firing rate, and stability of each place cell was compared across groups. Pathology was assessed by immunohistochemical staining, and a deep neural network approach was used to count cell profiles. RESULTS: Aged TgF344-AD rats exhibited hippocampal amyloid-ß deposition, and a significant increase in Iba1 immunoreactivity and microglia cell counts. Place cells from WT and TgF344-AD rat showed equivalent spatial information, in-field firing rates, and place field stability when initially exposed to the arena. However, by day 3, the place cells in aged WT rats showed characteristic spatial tuning as evidenced by higher spatial information content, stability, and in-field firing rates, an effect not seen in TgF344-AD rats. CONCLUSION: These findings support the notion that altered electrophysiological properties of place cells may contribute to the learning and memory deficits observed in AD.

Salicylic acid inducible nucleocytoplasmic shuttling of NPR1 fusion proteins in human cells.

Ligand inducible proteins that enable precise and reversible control of nuclear translocation of passenger proteins have broad applications ranging from genetic studies in mammals to therapeutics that target diseases such as cancer and diabetes. One of the drawbacks of the current translocation systems is that the ligands used to control nuclear localization are either toxic or prone to crosstalk with endogenous protein cascades within live animals. We sought to take advantage of salicylic acid (SA), a small molecule that has been extensively used in humans. In plants, SA functions as a hormone that can mediate immunity and is sensed by the nonexpressor of pathogenesis-related (NPR) proteins. Although it is well recognized that nuclear translocation of NPR1 is essential to promoting immunity in plants, the exact subdomain of Arabidopsis thaliana NPR1 (AtNPR1) essential for SA-mediated nuclear translocation is controversial. Here, we utilized the fluorescent protein mCherry as the reporter to investigate the ability of SA to induce nuclear translocation of the full-length NPR1 protein or its C-terminal transactivation (TAD) domain using HEK293 cells as a heterologous system. HEK293 cells lack accessory plant proteins including NPR3/NPR4 and are thus ideally suited for studying the impact of SA-induced changes in NPR1. Our results obtained using a stable expression system show that the TAD of AtNPR1 is sufficient to enable the reversible SA-mediated nuclear translocation of mCherry. Our studies advance a basic understanding of nuclear translocation mediated by the TAD of AtNPR1 and uncover a biotechnological tool for SA-mediated nuclear localization.

Whole-brain tissue mapping toolkit using large-scale highly multiplexed immunofluorescence imaging and deep neural networks.

Mapping biological processes in brain tissues requires piecing together numerous histological observations of multiple tissue samples. We present a direct method that generates readouts for a comprehensive panel of biomarkers from serial whole-brain slices, characterizing all major brain cell types, at scales ranging from subcellular compartments, individual cells, local multi-cellular niches, to whole-brain regions from each slice. We use iterative cycles of optimized 10-plex immunostaining with 10-color epifluorescence imaging to accumulate highly enriched image datasets from individual whole-brain slices, from which seamless signal-corrected mosaics are reconstructed. Specific fluorescent signals of interest are isolated computationally, rejecting autofluorescence, imaging noise, cross-channel bleed-through, and cross-labeling. Reliable large-scale cell detection and segmentation are achieved using deep neural networks. Cell phenotyping is performed by analyzing unique biomarker combinations over appropriate subcellular compartments. This approach can accelerate pre-clinical drug evaluation and system-level brain histology studies by simultaneously profiling multiple biological processes in their native anatomical context.

Artificial intelligence and machine learning in nephropathology.

Artificial intelligence (AI) for the purpose of this review is an umbrella term for technologies emulating a nephropathologist's ability to extract information on diagnosis, prognosis, and therapy responsiveness from native or transplant kidney biopsies. Although AI can be used to analyze a wide variety of biopsy-related data, this review focuses on whole slide images traditionally used in nephropathology. AI applications in nephropathology have recently become available through several advancing technologies, including (i) widespread introduction of glass slide scanners, (ii) data servers in pathology departments worldwide, and (iii) through greatly improved computer hardware to enable AI training. In this review, we explain how AI can enhance the reproducibility of nephropathology results for certain parameters in the context of precision medicine using advanced architectures, such as convolutional neural networks, that are currently the state of the art in machine learning software for this task. Because AI applications in nephropathology are still in their infancy, we show the power and potential of AI applications mostly in the example of oncopathology. Moreover, we discuss the technological obstacles as well as the current stakeholder and regulatory concerns about developing AI applications in nephropathology from the perspective of nephropathologists and the wider nephrology community. We expect the gradual introduction of these technologies into routine diagnostics and research for selective tasks, suggesting that this technology will enhance the performance of nephropathologists rather than making them redundant.

Automated Classification of Apoptosis in Phase Contrast Microscopy Using Capsule Network.

Automatic and accurate classification of apoptosis, or programmed cell death, will facilitate cell biology research. The state-of-the-art approaches in apoptosis classification use deep convolutional neural networks (CNNs). However, these networks are not efficient in encoding the part-whole relationships, thus requiring a large number of training samples to achieve robust generalization. This paper proposes an efficient variant of capsule networks (CapsNets) as an alternative to CNNs. Extensive experimental results demonstrate that the proposed CapsNets achieve competitive performances in target cell apoptosis classification, while significantly outperforming CNNs when the number of training samples is small. To utilize temporal information within microscopy videos, we propose a recurrent CapsNet constructed by stacking a CapsNet and a bi-directional long short-term recurrent structure. Our experiments show that when considering temporal constraints, the recurrent CapsNet achieves 93.8% accuracy and makes significantly more consistent prediction than NNs.

Defining potency of CAR+ T cells: Fast and furious or slow and steady.

Genetically engineered T cells that express chimeric antigen receptors (CAR+) are heterogeneous and thus, understanding the immunotherapeutic efficacy remains a challenge in adoptive cell therapy. We developed a high-throughput single-cell methodology, Timelapse Imaging Microscopy In Nanowell Grids (TIMING) to monitor interactions between immune cells and tumor cells in vitro. Using TIMING we demonstrated that CD4+ CAR+ T cells participate in multi-killing and benefit from improved resistance to activation induced cell death in comparison to CD8+ CAR+ T cells. For both subsets of cells, effector cell fate at the single-cell level was dependent on functional activation through multiple tumor cells.

TIMING 2.0: high-throughput single-cell profiling of dynamic cell-cell interactions by time-lapse imaging microscopy in nanowell grids.

MOTIVATION: Automated profiling of cell-cell interactions from high-throughput time-lapse imaging microscopy data of cells in nanowell grids (TIMING) has led to fundamental insights into cell-cell interactions in immunotherapy. This application note aims to enable widespread adoption of TIMING by (i) enabling the computations to occur on a desktop computer with a graphical processing unit instead of a server; (ii) enabling image acquisition and analysis to occur in the laboratory avoiding network data transfers to/from a server and (iii) providing a comprehensive graphical user interface. RESULTS: On a desktop computer, TIMING 2.0 takes 5 s/block/image frame, four times faster than our previous method on the same computer, and twice as fast as our previous method (TIMING) running on a Dell PowerEdge server. The cell segmentation accuracy (f-number = 0.993) is superior to our previous method (f-number = 0.821). A graphical user interface provides the ability to inspect the video analysis results, make corrective edits efficiently (one-click editing of an entire nanowell video sequence in 5-10 s) and display a summary of the cell killing efficacy measurements. AVAILABILITY AND IMPLEMENTATION: Open source Python software (GPL v3 license), instruction manual, sample data and sample results are included with the Supplement (https://github.com/RoysamLab/TIMING2). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Placing Sites on the Edge of Planar Silicon Microelectrodes Enhances Chronic Recording Functionality.

OBJECTIVE: This study aims to identify the impact of using edge sites over center sites on a planar silicon microelectrode array. METHODS: We used custom-designed, silicon-substrate multisite microelectrode arrays with sites on the center, edge, and tip. We compared their single unit recording capability, noise level, impedance, and histology to identify the differences between each site location. Wide and narrow devices were used to evaluate if the differences are consistent and meet theoretical expectations. RESULTS: On the wide device, significantly more number of edge sites were functional than center sites over the course of 8 weeks with generally higher signal-to-noise amplitude ratio. On the narrow device, edge sites also performed generally better than center sites, but the differences were not significant and smaller than wide devices. The data from the tip sites were inconclusive. CONCLUSION: Edge sites outperformed center sites in terms of single unit recording capability. This benefit decreased as the device gets narrower and the distance to center sites decreases. SIGNIFICANCE: We showed that a simple alteration to the site placement can greatly enhance the functionality of silicon microelectrodes. This study promotes the idea that not only the substrate but also the site architecture needs attention to lengthen the lifetime of neural implants.

Single-cell profiling of dynamic cytokine secretion and the phenotype of immune cells.

Natural killer (NK) cells are a highly heterogeneous population of innate lymphocytes that constitute our first line of defense against several types of tumors and microbial infections. Understanding the heterogeneity of these lymphocytes requires the ability to integrate their underlying phenotype with dynamic functional behaviors. We have developed and validated a single-cell methodology that integrates cellular phenotyping and dynamic cytokine secretion based on nanowell arrays and bead-based molecular biosensors. We demonstrate the robust passivation of the polydimethylsiloxane (PDMS)-based nanowells arrays with polyethylene glycol (PEG) and validated our assay by comparison to enzyme-linked immunospot (ELISPOT) assays. We used numerical simulations to optimize the molecular density of antibodies on the surface of the beads as a function of the capture efficiency of cytokines within an open-well system. Analysis of hundreds of individual human peripheral blood NK cells profiled ex vivo revealed that CD56dimCD16+ NK cells are immediate secretors of interferon gamma (IFN-γ) upon activation by phorbol 12-myristate 13-acetate (PMA) and ionomycin (< 3 h), and that there was no evidence of cooperation between NK cells leading to either synergistic activation or faster IFN-γ secretion. Furthermore, we observed that both the amount and rate of IFN-γ secretion from individual NK cells were donor-dependent. Collectively, these results establish our methodology as an investigational tool for combining phenotyping and real-time protein secretion of individual cells in a high-throughput manner.

Morphologically constrained spectral unmixing by dictionary learning for multiplex fluorescence microscopy.

MOTIVATION: Current spectral unmixing methods for multiplex fluorescence microscopy have a limited ability to cope with high spectral overlap as they only analyze spectral information over individual pixels. Here, we present adaptive Morphologically Constrained Spectral Unmixing (MCSU) algorithms that overcome this limitation by exploiting morphological differences between sub-cellular structures, and their local spatial context. RESULTS: The proposed method was effective at improving spectral unmixing performance by exploiting: (i) a set of dictionary-based models for object morphologies learned from the image data; and (ii) models of spatial context learned from the image data using a total variation algorithm. The method was evaluated on multi-spectral images of multiplex-labeled pancreatic ductal adenocarcinoma (PDAC) tissue samples. The former constraint ensures that neighbouring pixels correspond to morphologically similar structures, and the latter constraint ensures that neighbouring pixels have similar spectral signatures. The average Mean Squared Error (MSE) and Signal Reconstruction Error (SRE) ratio of the proposed method was 39.6% less and 8% more, respectively, compared to the best of all other algorithms that do not exploit these spatial constraints. AVAILABILITY AND IMPLEMENTATION: Open source software (MATLAB). CONTACT: broysam@central.uh.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Binge alcohol alters exercise-driven neuroplasticity.

Exercise is increasingly being used as a treatment for alcohol use disorders (AUD), but the interactive effects of alcohol and exercise on the brain remain largely unexplored. Alcohol damages the brain, in part by altering glial functioning. In contrast, exercise promotes glial health and plasticity. In the present study, we investigated whether binge alcohol would attenuate the effects of subsequent exercise on glia. We focused on the medial prefrontal cortex (mPFC), an alcohol-vulnerable region that also undergoes neuroplastic changes in response to exercise. Adult female Long-Evans rats were gavaged with ethanol (25% w/v) every 8h for 4days. Control animals received an isocaloric, non-alcohol diet. After 7days of abstinence, rats remained sedentary or exercised for 4weeks. Immunofluorescence was then used to label microglia, astrocytes, and neurons in serial tissue sections through the mPFC. Confocal microscope images were processed using FARSIGHT, a computational image analysis toolkit capable of automated analysis of cell number and morphology. We found that exercise increased the number of microglia in the mPFC in control animals. Binged animals that exercised, however, had significantly fewer microglia. Furthermore, computational arbor analytics revealed that the binged animals (regardless of exercise) had microglia with thicker, shorter arbors and significantly less branching, suggestive of partial activation. We found no changes in the number or morphology of mPFC astrocytes. We conclude that binge alcohol exerts a prolonged effect on morphology of mPFC microglia and limits the capacity of exercise to increase their numbers.

Unsupervised Discovery of Subspace Trends.

This paper presents unsupervised algorithms for discovering previously unknown subspace trends in high-dimensional data sets without the benefit of prior information. A subspace trend is a sustained pattern of gradual/progressive changes within an unknown subset of feature dimensions. A fundamental challenge to subspace trend discovery is the presence of irrelevant data dimensions, noise, outliers, and confusion from multiple subspace trends driven by independent factors that are mixed in with each other. These factors can obscure the trends in conventional dimension reduction & projection based data visualizations. To overcome these limitations, we propose a novel graph-theoretic neighborhood similarity measure for detecting concordant progressive changes across data dimensions. Using this measure, we present an unsupervised algorithm for trend-relevant feature selection, subspace trend discovery, quantification of trend strength, and validation. Our method successfully identified verifiable subspace trends in diverse synthetic and real-world biomedical datasets. Visualizations derived from the selected trend-relevant features revealed biologically meaningful hidden subspace trend(s) that were obscured by irrelevant features and noise. Although our examples are drawn from the biological domain, the proposed algorithm is broadly applicable to exploratory analysis of high-dimensional data including visualization, hypothesis generation, knowledge discovery, and prediction in diverse other applications.

Automated profiling of individual cell-cell interactions from high-throughput time-lapse imaging microscopy in nanowell grids (TIMING).

MOTIVATION: There is a need for effective automated methods for profiling dynamic cell-cell interactions with single-cell resolution from high-throughput time-lapse imaging data, especially, the interactions between immune effector cells and tumor cells in adoptive immunotherapy. RESULTS: Fluorescently labeled human T cells, natural killer cells (NK), and various target cells (NALM6, K562, EL4) were co-incubated on polydimethylsiloxane arrays of sub-nanoliter wells (nanowells), and imaged using multi-channel time-lapse microscopy. The proposed cell segmentation and tracking algorithms account for cell variability and exploit the nanowell confinement property to increase the yield of correctly analyzed nanowells from 45% (existing algorithms) to 98% for wells containing one effector and a single target, enabling automated quantification of cell locations, morphologies, movements, interactions, and deaths without the need for manual proofreading. Automated analysis of recordings from 12 different experiments demonstrated automated nanowell delineation accuracy >99%, automated cell segmentation accuracy >95%, and automated cell tracking accuracy of 90%, with default parameters, despite variations in illumination, staining, imaging noise, cell morphology, and cell clustering. An example analysis revealed that NK cells efficiently discriminate between live and dead targets by altering the duration of conjugation. The data also demonstrated that cytotoxic cells display higher motility than non-killers, both before and during contact. CONTACT: broysam@central.uh.edu or nvaradar@central.uh.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Quantitative 3-D analysis of GFAP labeled astrocytes from fluorescence confocal images.

BACKGROUND: There is a need for effective computational methods for quantifying the three-dimensional (3-D) spatial distribution, cellular arbor morphologies, and the morphological diversity of brain astrocytes to support quantitative studies of astrocytes in health, injury, and disease. NEW METHOD: Confocal fluorescence microscopy of multiplex-labeled (GFAP, DAPI) brain tissue is used to perform imaging of astrocytes in their tissue context. The proposed computational method identifies the astrocyte cell nuclei, and reconstructs their arbors using a local priority based parallel (LPP) tracing algorithm. Quantitative arbor measurements are extracted using Scorcioni's L-measure, and profiled by unsupervised harmonic co-clustering to reveal the morphological diversity. RESULTS: The proposed method identifies astrocyte nuclei, generates 3-D reconstructions of their arbors, and extracts quantitative arbor measurements, enabling a morphological grouping of the cell population. COMPARISON WITH EXISTING METHODS: Our method enables comprehensive spatial and morphological profiling of astrocyte populations in brain tissue for the first time, and overcomes limitations of prior methods. Visual proofreading of the results indicate a >95% accuracy in identifying astrocyte nuclei. The arbor reconstructions exhibited 3.2% fewer erroneous jumps in tracing, and 17.7% fewer false segments compared to the widely used fast-marching method that resulted in 9% jumps and 20.8% false segments. CONCLUSIONS: The proposed method can be used for large-scale quantitative studies of brain astrocyte distribution and morphology.

Population-scale three-dimensional reconstruction and quantitative profiling of microglia arbors.

MOTIVATION: The arbor morphologies of brain microglia are important indicators of cell activation. This article fills the need for accurate, robust, adaptive and scalable methods for reconstructing 3-D microglial arbors and quantitatively mapping microglia activation states over extended brain tissue regions. RESULTS: Thick rat brain sections (100-300 µm) were multiplex immunolabeled for IBA1 and Hoechst, and imaged by step-and-image confocal microscopy with automated 3-D image mosaicing, producing seamless images of extended brain regions (e.g. 5903 × 9874 × 229 voxels). An over-complete dictionary-based model was learned for the image-specific local structure of microglial processes. The microglial arbors were reconstructed seamlessly using an automated and scalable algorithm that exploits microglia-specific constraints. This method detected 80.1 and 92.8% more centered arbor points, and 53.5 and 55.5% fewer spurious points than existing vesselness and LoG-based methods, respectively, and the traces were 13.1 and 15.5% more accurate based on the DIADEM metric. The arbor morphologies were quantified using Scorcioni's L-measure. Coifman's harmonic co-clustering revealed four morphologically distinct classes that concord with known microglia activation patterns. This enabled us to map spatial distributions of microglial activation and cell abundances. AVAILABILITY AND IMPLEMENTATION: Experimental protocols, sample datasets, scalable open-source multi-threaded software implementation (C++, MATLAB) in the electronic supplement, and website (www.farsight-toolkit.org). http://www.farsight-toolkit.org/wiki/Population-scale_Three-dimensional_Reconstruction_and_Quanti-tative_Profiling_of_Microglia_Arbors CONTACT: broysam@central.uh.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.