A community-developed open-source computational ecosystem for big neuro data

Tractometry of the Human Connectome Project: resources and insights

Introduction

The Human Connectome Project (HCP) has become a keystone dataset in human neuroscience, with a plethora of important applications in advancing brain imaging methods and an understanding of the human brain. We focused on tractometry of HCP diffusion-weighted MRI (dMRI) data.

Methods

We used an open-source software library (pyAFQ; https://yeatmanlab.github.io/pyAFQ) to perform probabilistic tractography and delineate the major white matter pathways in the HCP subjects that have a complete dMRI acquisition (n = 1,041). We used diffusion kurtosis imaging (DKI) to model white matter microstructure in each voxel of the white matter, and extracted tract profiles of DKI-derived tissue properties along the length of the tracts. We explored the empirical properties of the data: first, we assessed the heritability of DKI tissue properties using the known genetic linkage of the large number of twin pairs sampled in HCP. Second, we tested the ability of tractometry to serve as the basis for predictive models of individual characteristics (e.g., age, crystallized/fluid intelligence, reading ability, etc.), compared to local connectome features. To facilitate the exploration of the dataset we created a new web-based visualization tool and use this tool to visualize the data in the HCP tractometry dataset. Finally, we used the HCP dataset as a test-bed for a new technological innovation: the TRX file-format for representation of dMRI-based streamlines.

Results

We released the processing outputs and tract profiles as a publicly available data resource through the AWS Open Data program's Open Neurodata repository. We found heritability as high as 0.9 for DKI-based metrics in some brain pathways. We also found that tractometry extracts as much useful information about individual differences as the local connectome method. We released a new web-based visualization tool for tractometry-"Tractoscope" (https://nrdg.github.io/tractoscope). We found that the TRX files require considerably less disk space-a crucial attribute for large datasets like HCP. In addition, TRX incorporates a specification for grouping streamlines, further simplifying tractometry analysis.

Morphomics via next-generation electron microscopy

The living body is composed of innumerable fine and complex structures. Although these structures have been studied in the past, a vast amount of information pertaining to them still remains unknown. When attempting to observe these ultra-structures, the use of electron microscopy (EM) has become indispensable. However, conventional EM settings are limited to a narrow tissue area, which can bias observations. Recently, new trends in EM research have emerged, enabling coverage of far broader, nano-scale fields of view for two-dimensional wide areas and three-dimensional large volumes. Moreover, cutting-edge bioimage informatics conducted via deep learning has accelerated the quantification of complex morphological bioimages. Taken together, these technological and analytical advances have led to the comprehensive acquisition and quantification of cellular morphology, which now arises as a new omics science termed 'morphomics'.

Ethics Along the Continuum of Research Involving Persons with Disorders of Consciousness

Interest in disorders of consciousness (DoC) has grown substantially over the past decade and has illuminated the importance of improving understanding of DoC biology; care needs (use of monitoring, performance of interventions, and provision of emotional support); treatment options to promote recovery; and outcome prediction. Exploration of these topics requires awareness of numerous ethics considerations related to rights and resources. The Curing Coma Campaign Ethics Working Group used its expertise in neurocritical care, neuropalliative care, neuroethics, neuroscience, philosophy, and research to formulate an informal review of ethics considerations along the continuum of research involving persons with DoC related to the following: (1) study design; (2) comparison of risks versus benefits; (3) selection of inclusion and exclusion criteria; (4) screening, recruitment, and enrollment; (5) consent; (6) data protection; (7) disclosure of results to surrogates and/or legally authorized representatives; (8) translation of research into practice; (9) identification and management of conflicts of interest; (10) equity and resource availability; and (11) inclusion of minors with DoC in research. Awareness of these ethics considerations when planning and performing research involving persons with DoC will ensure that the participant rights are respected while maximizing the impact and meaningfulness of the research, interpretation of outcomes, and communication of results.

A protocol for visualization of murine in situ neurovascular interfaces

Mapping cranial vasculature and adjacent neurovascular interfaces in their entirety will enhance our understanding of central nervous system function in any physiologic state. We present a workflow to visualize in situ murine vasculature and surrounding cranial structures using terminal polymer casting of vessels, iterative sample processing and image acquisition, and automated image registration and processing. While this method does not obtain dynamic imaging due to mouse sacrifice, these studies can be performed before sacrifice and processed with other acquired images. For complete details on the use and execution of this protocol, please refer to Rosenblum et al.1.

Merged magnetic resonance and light sheet microscopy of the whole mouse brain

We have developed workflows to align 3D magnetic resonance histology (MRH) of the mouse brain with light sheet microscopy (LSM) and 3D delineations of the same specimen. We start with MRH of the brain in the skull with gradient echo and diffusion tensor imaging (DTI) at 15 μm isotropic resolution which is ~ 1,000 times higher than that of most preclinical MRI. Connectomes are generated with superresolution tract density images of ~5 μm. Brains are cleared, stained for selected proteins, and imaged by LSM at 1.8 μm/pixel. LSM data are registered into the reference MRH space with labels derived from the ABA common coordinate framework. The result is a high-dimensional integrated volume with registration (HiDiver) with alignment precision better than 50 µm. Throughput is sufficiently high that HiDiver is being used in quantitative studies of the impact of gene variants and aging on mouse brain cytoarchitecture and connectomics.

Use of Computation Ecosystems to Analyze the Kidney-Heart Crosstalk

The identification of mediators for physiologic processes, correlation of molecular processes, or even pathophysiological processes within a single organ such as the kidney or heart has been extensively studied to answer specific research questions using organ-centered approaches in the past 50 years. However, it has become evident that these approaches do not adequately complement each other and display a distorted single-disease progression, lacking holistic multilevel/multidimensional correlations. Holistic approaches have become increasingly significant in understanding and uncovering high dimensional interactions and molecular overlaps between different organ systems in the pathophysiology of multimorbid and systemic diseases like cardiorenal syndrome because of pathological heart-kidney crosstalk. Holistic approaches to unraveling multimorbid diseases are based on the integration, merging, and correlation of extensive, heterogeneous, and multidimensional data from different data sources, both -omics and nonomics databases. These approaches aimed at generating viable and translatable disease models using mathematical, statistical, and computational tools, thereby creating first computational ecosystems. As part of these computational ecosystems, systems medicine solutions focus on the analysis of -omics data in single-organ diseases. However, the data-scientific requirements to address the complexity of multimodality and multimorbidity reach far beyond what is currently available and require multiphased and cross-sectional approaches. These approaches break down complexity into small and comprehensible challenges. Such holistic computational ecosystems encompass data, methods, processes, and interdisciplinary knowledge to manage the complexity of multiorgan crosstalk. Therefore, this review summarizes the current knowledge of kidney-heart crosstalk, along with methods and opportunities that arise from the novel application of computational ecosystems providing a holistic analysis on the example of kidney-heart crosstalk.

Reconstructing Network Dynamics of Coupled Discrete Chaotic Units from Data

Reconstructing network dynamics from data is crucial for predicting the changes in the dynamics of complex systems such as neuron networks; however, previous research has shown that the reconstruction is possible under strong constraints such as the need for lengthy data or small system size. Here, we present a recovery scheme blending theoretical model reduction and sparse recovery to identify the governing equations and the interactions of weakly coupled chaotic maps on complex networks, easing unrealistic constraints for real-world applications. Learning dynamics and connectivity lead to detecting critical transitions for parameter changes. We apply our technique to realistic neuronal systems with and without noise on a real mouse neocortex and artificial networks.

CLAIRE-Parallelized Diffeomorphic Image Registration for Large-Scale Biomedical Imaging Applications

We study the performance of CLAIRE—a diffeomorphic multi-node, multi-GPU image-registration algorithm and software—in large-scale biomedical imaging applications with billions of voxels. At such resolutions, most existing software packages for diffeomorphic image registration are prohibitively expensive. As a result, practitioners first significantly downsample the original images and then register them using existing tools. Our main contribution is an extensive analysis of the impact of downsampling on registration performance. We study this impact by comparing full-resolution registrations obtained with CLAIRE to lower resolution registrations for synthetic and real-world imaging datasets. Our results suggest that registration at full resolution can yield a superior registration quality—but not always. For example, downsampling a synthetic image from 10243 to 2563 decreases the Dice coefficient from 92% to 79%. However, the differences are less pronounced for noisy or low contrast high resolution images. CLAIRE allows us not only to register images of clinically relevant size in a few seconds but also to register images at unprecedented resolution in reasonable time. The highest resolution considered are CLARITY images of size 2816×3016×1162. To the best of our knowledge, this is the first study on image registration quality at such resolutions.

How innovations in methodology offer new prospects for volume electron microscopy

Detailed knowledge of biological structure has been key in understanding biology at several levels of organisation, from organs to cells and proteins. Volume electron microscopy (volume EM) provides high resolution 3D structural information about tissues on the nanometre scale. However, the throughput rate of conventional electron microscopes has limited the volume size and number of samples that can be imaged. Recent improvements in methodology are currently driving a revolution in volume EM, making possible the structural imaging of whole organs and small organisms. In turn, these recent developments in image acquisition have created or stressed bottlenecks in other parts of the pipeline, like sample preparation, image analysis and data management. While the progress in image analysis is stunning due to the advent of automatic segmentation and server‐based annotation tools, several challenges remain. Here we discuss recent trends in volume EM, emerging methods for increasing throughput and implications for sample preparation, image analysis and data management.

Connectomics Annotation Metadata Standardization for Increased Accessibility and Queryability

Neuroscientists can leverage technological advances to image neural tissue across a range of different scales, potentially forming the basis for the next generation of brain atlases and circuit reconstructions at submicron resolution, using Electron Microscopy and X-ray Microtomography modalities. However, there is variability in data collection, annotation, and storage approaches, which limits effective comparative and secondary analysis. There has been great progress in standardizing interfaces for large-scale spatial image data, but more work is needed to standardize annotations, especially metadata associated with neuroanatomical entities. Standardization will enable validation, sharing, and replication, greatly amplifying investment throughout the connectomics community. We share key design considerations and a usecase developed for metadata for a recent large-scale dataset.

Is Neuroscience FAIR? A Call for Collaborative Standardisation of Neuroscience Data

In this perspective article, we consider the critical issue of data and other research object standardisation and, specifically, how international collaboration, and organizations such as the International Neuroinformatics Coordinating Facility (INCF) can encourage that emerging neuroscience data be Findable, Accessible, Interoperable, and Reusable (FAIR). As neuroscientists engaged in the sharing and integration of multi-modal and multiscale data, we see the current insufficiency of standards as a major impediment in the Interoperability and Reusability of research results. We call for increased international collaborative standardisation of neuroscience data to foster integration and efficient reuse of research objects.

A call for comparing theories of consciousness and data sharing

Merker, Williford, and Rudrauf make several arguments against the integrated information theory of consciousness; whereas some have merit, their conclusion that the theory should be discarded is premature. Coming years promise advances in the empirical study of consciousness, and only after theories are independently tested with shared data can they be ruled in or out. We propose future research directions.

The Brain Observatory Storage Service and Database (BossDB): A Cloud-Native Approach for Petascale Neuroscience Discovery

Technological advances in imaging and data acquisition are leading to the development of petabyte-scale neuroscience image datasets. These large-scale volumetric datasets pose unique challenges since analyses often span the entire volume, requiring a unified platform to access it. In this paper, we describe the Brain Observatory Storage Service and Database (BossDB), a cloud-based solution for storing and accessing petascale image datasets. BossDB provides support for data ingest, storage, visualization, and sharing through a RESTful Application Programming Interface (API). A key feature is the scalable indexing of spatial data and automatic and manual annotations to facilitate data discovery. Our project is open source and can be easily and cost effectively used for a variety of modalities and applications, and has effectively worked with datasets over a petabyte in size.

Visualization of Speech Perception Analysis via Phoneme Alignment: A Pilot Study

Objective: Speech tests assess the ability of people with hearing loss to comprehend speech with a hearing aid or cochlear implant. The tests are usually at the word or sentence level. However, few tests analyze errors at the phoneme level. So, there is a need for an automated program to visualize in real time the accuracy of phonemes in these tests. Method: The program reads in stimulus-response pairs and obtains their phonemic representations from an open-source digital pronouncing dictionary. The stimulus phonemes are aligned with the response phonemes via a modification of the Levenshtein Minimum Edit Distance algorithm. Alignment is achieved via dynamic programming with modified costs based on phonological features for insertion, deletions and substitutions. The accuracy for each phoneme is based on the F1-score. Accuracy is visualized with respect to place and manner (consonants) or height (vowels). Confusion matrices for the phonemes are used in an information transfer analysis of ten phonological features. A histogram of the information transfer for the features over a frequency-like range is presented as a phonemegram. Results: The program was applied to two datasets. One consisted of test data at the sentence and word levels. Stimulus-response sentence pairs from six volunteers with different degrees of hearing loss and modes of amplification were analyzed. Four volunteers listened to sentences from a mobile auditory training app while two listened to sentences from a clinical speech test. Stimulus-response word pairs from three lists were also analyzed. The other dataset consisted of published stimulus-response pairs from experiments of 31 participants with cochlear implants listening to 400 Basic English Lexicon sentences via different talkers at four different SNR levels. In all cases, visualization was obtained in real time. Analysis of 12,400 actual and random pairs showed that the program was robust to the nature of the pairs. Conclusion: It is possible to automate the alignment of phonemes extracted from stimulus-response pairs from speech tests in real time. The alignment then makes it possible to visualize the accuracy of responses via phonological features in two ways. Such visualization of phoneme alignment and accuracy could aid clinicians and scientists.

Non-invasive in situ Visualization of the Murine Cranial Vasculature

Understanding physiologic and pathologic central nervous system function depends on our ability to map the entire in situ cranial vasculature and neurovascular interfaces. To accomplish this, we developed a non-invasive workflow to visualize murine cranial vasculature via polymer casting of vessels, iterative sample processing and micro-computed tomography, and automatic deformable image registration, feature extraction, and visualization. This methodology is applicable to any tissue and allows rapid exploration of normal and altered pathologic states.

Tentorial venous anatomy of mice and humans

We recently described a transtentorial venous system (TTVS), which to our knowledge was previously unknown, connecting venous drainage throughout the brain in humans. Prior to this finding, it was believed that the embryologic tentorial plexus regresses, resulting in a largely avascular tentorium. Our finding contradicted this understanding and necessitated further investigation into the development of the TTVS. Herein, we sought to investigate mice as a model to study the development of this system. First, using vascular casting and ex vivo micro-CT, we demonstrated that this TTVS is conserved in adult mice. Next, using high-resolution MRI, we identified the primitive tentorial venous plexus in the murine embryo at day 14.5. We also found that, at this embryologic stage, the tentorial plexus drains the choroid plexus. Finally, using vascular casting and micro-CT, we found that the TTVS is the dominant venous drainage in the early postnatal period (P8). Herein, we demonstrated that the TTVS is conserved between mice and humans, and we present a longitudinal study of its development. In addition, our findings establish mice as a translational model for further study of this system and its relationship to intracranial physiology.

CONFIRMS: A Toolkit for Scalable, Black Box Connectome Assessment and Investigation

The nanoscale connectomics community has recently generated automated and semi-automated "wiring diagrams" of brain subregions from terabytes and petabytes of dense 3D neuroimagery. This process involves many challenging and imperfect technical steps, including dense 3D image segmentation, anisotropic nonrigid image alignment and coregistration, and pixel classification of each neuron and their individual synaptic connections. As data volumes continue to grow in size, and connectome generation becomes increasingly commonplace, it is important that the scientific community is able to rapidly assess the quality and accuracy of a connectome product to promote dataset analysis and reuse. In this work, we share our scalable toolkit for assessing the quality of a connectome reconstruction via targeted inquiry and large-scale graph analysis, and to provide insights into how such connectome proofreading processes may be improved and optimized in the future. We illustrate the applications and ecosystem on a recent reference dataset.Clinical relevance- Large-scale electron microscopy (EM) data offers a novel opportunity to characterize etiologies and neurological diseases and conditions at an unprecedented scale. EM is useful for low-level analyses such as biopsies; this increased scale offers new possibilities for research into areas such as neural networks if certain bottlenecks and problems are overcome.

An Integrated Toolkit for Extensible and Reproducible Neuroscience

As neuroimagery datasets continue to grow in size, the complexity of data analyses can require a detailed understanding and implementation of systems computer science for storage, access, processing, and sharing. Currently, several general data standards (e.g., Zarr, HDF5, precomputed) and purpose-built ecosystems (e.g., BossDB, CloudVolume, DVID, and Knossos) exist. Each of these systems has advantages and limitations and is most appropriate for different use cases. Using datasets that don’t fit into RAM in this heterogeneous environment is challenging, and significant barriers exist to leverage underlying research investments. In this manuscript, we outline our perspective for how to approach this challenge through the use of community provided, standardized interfaces that unify various computational backends and abstract computer science challenges from the scientist. We introduce desirable design patterns and share our reference implementation called intern.

Cellular anatomy of the mouse primary motor cortex

An essential step toward understanding brain function is to establish a structural framework with cellular resolution on which multi-scale datasets spanning molecules, cells, circuits and systems can be integrated and interpreted1. Here, as part of the collaborative Brain Initiative Cell Census Network (BICCN), we derive a comprehensive cell type-based anatomical description of one exemplar brain structure, the mouse primary motor cortex, upper limb area (MOp-ul). Using genetic and viral labelling, barcoded anatomy resolved by sequencing, single-neuron reconstruction, whole-brain imaging and cloud-based neuroinformatics tools, we delineated the MOp-ul in 3D and refined its sublaminar organization. We defined around two dozen projection neuron types in the MOp-ul and derived an input-output wiring diagram, which will facilitate future analyses of motor control circuitry across molecular, cellular and system levels. This work provides a roadmap towards a comprehensive cellular-resolution description of mammalian brain architecture.

Multimodal Atlas of the Murine Inner Ear: From Embryo to Adult

The inner ear is a complex organ housed within the petrous bone of the skull. Its intimate relationship with the brain enables the transmission of auditory and vestibular signals via cranial nerves. Development of this structure from neural crest begins in utero and continues into early adulthood. However, the anatomy of the murine inner ear has only been well-characterized from early embryogenesis to post-natal day 6. Inner ear and skull base development continue into the post-natal period in mice and early adulthood in humans. Traditional methods used to evaluate the inner ear in animal models, such as histologic sectioning or paint-fill and corrosion, cannot visualize this complex anatomy in situ. Further, as the petrous bone ossifies in the postnatal period, these traditional techniques become increasingly difficult. Advances in modern imaging, including high resolution Micro-CT and MRI, now allow for 3D visualization of the in situ anatomy of organs such as the inner ear. Here, we present a longitudinal atlas of the murine inner ear using high resolution ex vivo Micro-CT and MRI.

Dimension-reduction of dynamics on real-world networks with symmetry

We derive explicit formulae to quantify the Markov chain state-space compression, or lumping, that can be achieved in a broad range of dynamical processes on real-world networks, including models of epidemics and voting behaviour, by exploiting redundancies due to symmetries. These formulae are applied in a large-scale study of such symmetry-induced lumping in real-world networks, from which we identify specific networks for which lumping enables exact analysis that could not have been done on the full state-space. For most networks, lumping gives a state-space compression ratio of up to 10 7 , but the largest compression ratio identified is nearly 10 12 . Many of the highest compression ratios occur in animal social networks. We also present examples of types of symmetry found in real-world networks that have not been previously reported.

DotMotif: an open-source tool for connectome subgraph isomorphism search and graph queries

Recent advances in neuroscience have enabled the exploration of brain structure at the level of individual synaptic connections. These connectomics datasets continue to grow in size and complexity; methods to search for and identify interesting graph patterns offer a promising approach to quickly reduce data dimensionality and enable discovery. These graphs are often too large to be analyzed manually, presenting significant barriers to searching for structure and testing hypotheses. We combine graph database and analysis libraries with an easy-to-use neuroscience grammar suitable for rapidly constructing queries and searching for subgraphs and patterns of interest. Our approach abstracts many of the computer science and graph theory challenges associated with nanoscale brain network analysis and allows scientists to quickly conduct research at scale. We demonstrate the utility of these tools by searching for motifs on simulated data and real public connectomics datasets, and we share simple and complex structures relevant to the neuroscience community. We contextualize our findings and provide case studies and software to motivate future neuroscience exploration.

CUBIC-Cloud provides an integrative computational framework toward community-driven whole-mouse-brain mapping

Recent advancements in tissue clearing technologies have offered unparalleled opportunities for researchers to explore the whole mouse brain at cellular resolution. With the expansion of this experimental technique, however, a scalable and easy-to-use computational tool is in demand to effectively analyze and integrate whole-brain mapping datasets. To that end, here we present CUBIC-Cloud, a cloud-based framework to quantify, visualize, and integrate mouse brain data. CUBIC-Cloud is a fully automated system where users can upload their whole-brain data, run analyses, and publish the results. We demonstrate the generality of CUBIC-Cloud by a variety of applications. First, we investigated the brain-wide distribution of five cell types. Second, we quantified Aβ plaque deposition in Alzheimer's disease model mouse brains. Third, we reconstructed a neuronal activity profile under LPS-induced inflammation by c-Fos immunostaining. Last, we show brain-wide connectivity mapping by pseudotyped rabies virus. Together, CUBIC-Cloud provides an integrative platform to advance scalable and collaborative whole-brain mapping.

CEM500K, a large-scale heterogeneous unlabeled cellular electron microscopy image dataset for deep learning

Automated segmentation of cellular electron microscopy (EM) datasets remains a challenge. Supervised deep learning (DL) methods that rely on region-of-interest (ROI) annotations yield models that fail to generalize to unrelated datasets. Newer unsupervised DL algorithms require relevant pre-training images, however, pre-training on currently available EM datasets is computationally expensive and shows little value for unseen biological contexts, as these datasets are large and homogeneous. To address this issue, we present CEM500K, a nimble 25 GB dataset of 0.5 × 106 unique 2D cellular EM images curated from nearly 600 three-dimensional (3D) and 10,000 two-dimensional (2D) images from >100 unrelated imaging projects. We show that models pre-trained on CEM500K learn features that are biologically relevant and resilient to meaningful image augmentations. Critically, we evaluate transfer learning from these pre-trained models on six publicly available and one newly derived benchmark segmentation task and report state-of-the-art results on each. We release the CEM500K dataset, pre-trained models and curation pipeline for model building and further expansion by the EM community. Data and code are available at https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10592/ and https://git.io/JLLTz.

Upscaling X-ray nanoimaging to macroscopic specimens

Upscaling X-ray nanoimaging to macroscopic specimens has the potential for providing insights across multiple length scales, but its feasibility has long been an open question. By combining the imaging requirements and existing proof-of-principle examples in large-specimen preparation, data acquisition and reconstruction algorithms, the authors provide imaging time estimates for howX-ray nanoimaging can be scaled to macroscopic specimens. To arrive at this estimate, a phase contrast imaging model that includes plural scattering effects is used to calculate the required exposure and corresponding radiation dose. The coherent X-ray flux anticipated from upcoming diffraction-limited light sources is then considered. This imaging time estimation is in particular applied to the case of the connectomes of whole mouse brains. To image the connectome of the whole mouse brain, electron microscopy connectomics might require years, whereas optimized X-ray microscopy connectomics could reduce this to one week. Furthermore, this analysis points to challenges that need to be overcome (such as increased X-ray detector frame rate) and opportunities that advances in artificial-intelligence-based 'smart' scanning might provide. While the technical advances required are daunting, it is shown that X-ray microscopy is indeed potentially applicable to nanoimaging of millimetre- or even centimetre-size specimens.

Multi-Node Multi-GPU Diffeomorphic Image Registration for Large-Scale Imaging Problems

We present a Gauss-Newton-Krylov solver for large deformation diffeomorphic image registration. We extend the publicly available CLAIRE library to multi-node multi-graphics processing unit (GPUs) systems and introduce novel algorithmic modifications that significantly improve performance. Our contributions comprise (i) a new preconditioner for the reduced-space Gauss-Newton Hessian system, (ii) a highly-optimized multi-node multi-GPU implementation exploiting device direct communication for the main computational kernels (interpolation, high-order finite difference operators and Fast-Fourier-Transform), and (iii) a comparison with state-of-the-art CPU and GPU implementations. We solve a 256³-resolution image registration problem in five seconds on a single NVIDIA Tesla V100, with a performance speedup of 70% compared to the state-of-the-art. In our largest run, we register 2048³ resolution images (25 B unknowns; approximately 152× larger than the largest problem solved in state-of-the-art GPU implementations) on 64 nodes with 256 GPUs on TACC's Longhorn system.

Application of the hierarchical bootstrap to multi-level data in neuroscience

A common feature in many neuroscience datasets is the presence of hierarchical data structures, most commonly recording the activity of multiple neurons in multiple animals across multiple trials. Accordingly, the measurements constituting the dataset are not independent, even though the traditional statistical analyses often applied in such cases (e.g., Student's t-test) treat them as such. The hierarchical bootstrap has been shown to be an effective tool to accurately analyze such data and while it has been used extensively in the statistical literature, its use is not widespread in neuroscience - despite the ubiquity of hierarchical datasets. In this paper, we illustrate the intuitiveness and utility of this approach to analyze hierarchically nested datasets. We use simulated neural data to show that traditional statistical tests can result in a false positive rate of over 45%, even if the Type-I error rate is set at 5%. While summarizing data across non-independent points (or lower levels) can potentially fix this problem, this approach greatly reduces the statistical power of the analysis. The hierarchical bootstrap, when applied sequentially over the levels of the hierarchical structure, keeps the Type-I error rate within the intended bound and retains more statistical power than summarizing methods. We conclude by demonstrating the effectiveness of the method in two real-world examples, first analyzing singing data in male Bengalese finches (Lonchura striata var. domestica) and second quantifying changes in behavior under optogenetic control in flies (Drosophila melanogaster).

Toward Community-Driven Big Open Brain Science: Open Big Data and Tools for Structure, Function, and Genetics

As acquiring bigger data becomes easier in experimental brain science, computational and statistical brain science must achieve similar advances to fully capitalize on these data. Tackling these problems will benefit from a more explicit and concerted effort to work together. Specifically, brain science can be further democratized by harnessing the power of community-driven tools, which both are built by and benefit from many different people with different backgrounds and expertise. This perspective can be applied across modalities and scales and enables collaborations across previously siloed communities.

A substrate for modular, extensible data-visualization

Background

As the scope of scientific questions increase and datasets grow larger, the visualization of relevant information correspondingly becomes more difficult and complex. Sharing visualizations amongst collaborators and with the public can be especially onerous, as it is challenging to reconcile software dependencies, data formats, and specific user needs in an easily accessible package.

Results

We present substrate, a data-visualization framework designed to simplify communication and code reuse across diverse research teams. Our platform provides a simple, powerful, browser-based interface for scientists to rapidly build effective three-dimensional scenes and visualizations. We aim to reduce the limitations of existing systems, which commonly prescribe a limited set of high-level components, that are rarely optimized for arbitrarily large data visualization or for custom data types.

Conclusions

To further engage the broader scientific community and enable seamless integration with existing scientific workflows, we also present pytri, a Python library that bridges the use of substrate with the ubiquitous scientific computing platform, Jupyter. Our intention is to lower the activation energy required to transition between exploratory data analysis, data visualization, and publication-quality interactive scenes.

Why Study the History of Neuroscience?

The history of neuroscience is the memory of the discipline and this memory depends on the study of the present traces of the past; the things left behind: artifacts, equipment, written documents, data books, photographs, memoirs, etc. History, in all of its definitions, is an integral part of neuroscience and I have used examples from the literature and my personal experience to illustrate the importance of the different aspects of history in neuroscience. Each time we talk about the brain, do an experiment, or write a research article, we are involved in history. Each published experiment becomes a historical document; it relies on past research (the "Introduction" section), procedures developed in the past ("Methods" section) and as soon as new data are published, they become history and become embedded into the history of the discipline ("Discussion" section). In order to be transparent and able to be replicated, each experiment requires its own historical archive. Studying history means researching books, documents and objects in libraries, archives, and museums. It means looking at data books, letters and memos, talking to scientists, and reading biographies and autobiographies. History can be made relevant by integrating historical documents into classes and by using historical websites. Finally, conducting historical research can be interesting, entertaining, and can lead to travel to out-of-the-way and exotic places and meeting interesting people.