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Understanding the cortical organization of the human brain requires interpretable descriptors for distinct structural and functional imaging data. 3D polarized light imaging (3D-PLI) is an imaging modality for visualizing fiber architecture in postmortem brains with high resolution that also captures the presence of cell bodies, for example, to identify hippocampal subfields. The rich texture in 3D-PLI images, however, makes this modality particularly difficult to analyze and best practices for characterizing architectonic patterns still need to be established. In this work, we demonstrate a novel method to analyze the regional organization of the human hippocampus in 3D-PLI by combining recent advances in unfolding methods with deep texture features obtained using a self-supervised contrastive learning approach. We identify clusters in the representations that correspond well with classical descriptions of hippocampal subfields, lending validity to the developed methodology., Comment: Accepted to ISBI 2024

Machine learning models are commonly applied to human brain imaging datasets in an effort to associate function or structure with behaviour, health, or other individual phenotypes. Such models often rely on low-dimensional maps generated by complex processing pipelines. However, the numerical instabilities inherent to pipelines limit the fidelity of these maps and introduce computational bias. Monte Carlo Arithmetic, a technique for introducing controlled amounts of numerical noise, was used to perturb a structural connectome estimation pipeline, ultimately producing a range of plausible networks for each sample. The variability in the perturbed networks was captured in an augmented dataset, which was then used for an age classification task. We found that resampling brain networks across a series of such numerically perturbed outcomes led to improved performance in all tested classifiers, preprocessing strategies, and dimensionality reduction techniques. Importantly, we find that this benefit does not hinge on a large number of perturbations, suggesting that even minimally perturbing a dataset adds meaningful variance which can be captured in the subsequently designed models.

Human brain atlases provide spatial reference systems for data characterizing brain organization at different levels, coming from different brains. Cytoarchitecture is a basic principle of the microstructural organization of the brain, as regional differences in the arrangement and composition of neuronal cells are indicators of changes in connectivity and function. Automated scanning procedures and observer-independent methods are prerequisites to reliably identify cytoarchitectonic areas, and to achieve reproducible models of brain segregation. Time becomes a key factor when moving from the analysis of single regions of interest towards high-throughput scanning of large series of whole-brain sections. Here we present a new workflow for mapping cytoarchitectonic areas in large series of cell-body stained histological sections of human postmortem brains. It is based on a Deep Convolutional Neural Network (CNN), which is trained on a pair of section images with annotations, with a large number of un-annotated sections in between. The model learns to create all missing annotations in between with high accuracy, and faster than our previous workflow based on observer-independent mapping. The new workflow does not require preceding 3D-reconstruction of sections, and is robust against histological artefacts. It processes large data sets with sizes in the order of multiple Terabytes efficiently. The workflow was integrated into a web interface, to allow access without expertise in deep learning and batch computing. Applying deep neural networks for cytoarchitectonic mapping opens new perspectives to enable high-resolution models of brain areas, introducing CNNs to identify borders of brain areas., Comment: Preprint submitted to NeuroImage

Data analysis pipelines are known to be impacted by computational conditions, presumably due to the creation and propagation of numerical errors. While this process could play a major role in the current reproducibility crisis, the precise causes of such instabilities and the path along which they propagate in pipelines are unclear. We present Spot, a tool to identify which processes in a pipeline create numerical differences when executed in different computational conditions. Spot leverages system-call interception through ReproZip to reconstruct and compare provenance graphs without pipeline instrumentation. By applying Spot to the structural pre-processing pipelines of the Human Connectome Project, we found that linear and non-linear registration are the cause of most numerical instabilities in these pipelines, which confirms previous findings., Comment: 10 pages, 6 figures, 2 tables

Most segmentation methods in child brain MRI are supervised and are based on global intensity distributions of major brain structures. The successful implementation of a supervised approach depends on availability of an age-appropriate probabilistic brain atlas. For the study of early normal brain development, the construction of such a brain atlas remains a significant challenge. Moreover, using global intensity statistics leads to inaccurate detection of major brain tissue classes due to substantial intensity variations of MR signal within the constituent parts of early developing brain. In order to overcome these methodological limitations we develop a local, semi-supervised framework. It is based on Kernel Fisher Discriminant Analysis (KFDA) for pattern recognition, combined with an objective structural similarity index (SSIM) for perceptual image quality assessment. The proposed method performs optimal brain partitioning into subdomains having different average intensity values followed by SSIM-guided computation of separating surfaces between the constituent brain parts. The classified image subdomains are then stitched slice by slice via simulated annealing to form a global image of the classified brain. In this paper, we consider classification into major tissue classes (white matter and grey matter) and the cerebrospinal fluid and illustrate the proposed framework on examples of brain templates for ages 8 to 11 months and ages 44 to 60 months. We show that our method improves detection of the tissue classes by its comparison to state-of-the-art classification techniques known as Partial Volume Estimation., Comment: This manuscript was written by Nataliya Portman in the end of her postdoctoral tenure in 2014 and reviewed and edited by Paul-J Toussaint. 31 pages including Appendix, 14 figures. arXiv admin note: text overlap with arXiv:2005.03261

Shared high-performance computing (HPC) platforms, such as those provided by XSEDE and Compute Canada, enable researchers to carry out large-scale computational experiments at a fraction of the cost of the cloud. Most systems require the use of distributed filesystems (e.g. Lustre) for providing a highly multi-user, large capacity storage environment. These suffer performance penalties as the number of files increases due to network contention and metadata performance. We demonstrate how a combination of two technologies, Singularity and SquashFS, can help developers, integrators, architects, and scientists deploy large datasets (O(10M) files) on these shared systems with minimal performance limitations. The proposed integration enables more efficient access and indexing than normal file-based dataset installations, while providing transparent file access to users and processes. Furthermore, the approach does not require administrative privileges on the target system. While the examples studied here have been taken from the field of neuroimaging, the technologies adopted are not specific to that field. Currently, this solution is limited to read-only datasets. We propose the adoption of this technology for the consumption and dissemination of community datasets across shared computing resources., Comment: 5 pages, 2 figures, 2 tables. Submitted to PEARC 2020 conference

A lack of software reproducibility has become increasingly apparent in the last several years, calling into question the validity of scientific findings affected by published tools. Reproducibility issues may have numerous sources of error, including the underlying numerical stability of algorithms and implementations employed. Various forms of instability have been observed in neuroimaging, including across operating system versions, minor noise injections, and implementation of theoretically equivalent algorithms. In this paper we explore the effect of various perturbation methods on a typical neuroimaging pipeline through the use of i) targeted noise injections, ii) Monte Carlo Arithmetic, and iii) varying operating systems to identify the quality and severity of their impact. The work presented here demonstrates that even low order computational models such as the connectome estimation pipeline that we used are susceptible to noise. This suggests that stability is a relevant axis upon which tools should be compared, developed, or improved, alongside more commonly considered axes such as accuracy/biological feasibility or performance. The heterogeneity observed across participants clearly illustrates that stability is a property of not just the data or tools independently, but their interaction. Characterization of stability should therefore be evaluated for specific analyses and performed on a representative set of subjects for consideration in subsequent statistical testing. Additionally, identifying how this relationship scales to higher-order models is an exciting next step which will be explored. Finally, the joint application of perturbation methods with post-processing approaches such as bagging or signal normalization may lead to the development of more numerically stable analyses while maintaining sensitivity to meaningful variation., Comment: 9 pages, 5 figures, 1 table, paper published at IJHPCA

Neuroscience has been carried into the domain of big data and high performance computing (HPC) on the backs of initiatives in data collection and an increasingly compute-intensive tools. While managing HPC experiments requires considerable technical acumen, platforms and standards have been developed to ease this burden on scientists. While web-portals make resources widely accessible, data organizations such as the Brain Imaging Data Structure and tool description languages such as Boutiques provide researchers with a foothold to tackle these problems using their own datasets, pipelines, and environments. While these standards lower the barrier to adoption of HPC and cloud systems for neuroscience applications, they still require the consolidation of disparate domain-specific knowledge. We present Clowdr, a lightweight tool to launch experiments on HPC systems and clouds, record rich execution records, and enable the accessible sharing of experimental summaries and results. Clowdr uniquely sits between web platforms and bare-metal applications for experiment management by preserving the flexibility of do-it-yourself solutions while providing a low barrier for developing, deploying and disseminating neuroscientific analysis., Comment: 12 pages, 3 figures, 1 tool

Neural electromagnetic (EM) signals recorded non-invasively from individual human subjects vary in complexity and magnitude. Nonetheless, variation in neural activity has been difficult to quantify and interpret, due to complex, broad-band features in the frequency domain. Studying signals recorded with magnetoencephalography (MEG) from healthy young adult subjects while in resting and active states, a systematic framework inspired by thermodynamics is applied to neural EM signals. Despite considerable inter-subject variation in terms of spectral entropy and energy across time epochs, data support the existence of a robust and linear relationship defining an effective state equation, with higher energy and lower entropy in the resting state compared to active, consistently across subjects. Mechanisms underlying the emergence of relationships between empirically measured effective state functions are further investigated using a model network of coupled oscillators, suggesting an interplay between noise and coupling strength can account for coherent variation of empirically observed quantities. Taken together, the results show macroscopic neural observables follow a robust, non-trivial conservation rule for energy modulation and information generation., Comment: 6 pages, 4 figures

Random noise plays a beneficial role in cognitive processing and produces measurable improvement in simulations and biological agents' task performance. Stochastic facilitation, the phenomenon of additive noise improving signal transmission in complex systems, has been shown to occur in a variety of neural contexts. However, neuroscience analyses to date have not fully explored the colours that neural noise could be. The literature shows a 1/f pink noise power spectrum distribution at many levels, but many less rigourous studies assume white noise, with little justification of why that assumption is made. In this work, we briefly review the colours of noise and their useful applications in other fields. If we consider that noise is not so black and white, we could more colourfully regularize artificial neural networks and re-investigate some surprising results about how the brain benefits from noise., Comment: 4-page paper submitted to 2018 Conference on Cognitive Computational Neuroscience

In this paper, we provide an extensive overview of machine learning techniques applied to structural magnetic resonance imaging (MRI) data to obtain clinical classifiers. We specifically address practical problems commonly encountered in the literature, with the aim of helping researchers improve the application of these techniques in future works. Additionally, we survey how these algorithms are applied to a wide range of diseases and disorders (e.g. Alzheimer's disease (AD), Parkinson's disease (PD), autism, multiple sclerosis, traumatic brain injury, etc.) in order to provide a comprehensive view of the state of the art in different fields., Comment: 70 pages, 3 figures. First two authors share first authorship

Neuroscientists are now able to acquire data at staggering rates across spatiotemporal scales. However, our ability to capitalize on existing datasets, tools, and intellectual capacities is hampered by technical challenges. The key barriers to accelerating scientific discovery correspond to the FAIR data principles: findability, global access to data, software interoperability, and reproducibility/re-usability. We conducted a hackathon dedicated to making strides in those steps. This manuscript is a technical report summarizing these achievements, and we hope serves as an example of the effectiveness of focused, deliberate hackathons towards the advancement of our quickly-evolving field., Comment: 10 pages, 4 figures, hackathon report

We present Boutiques, a system to automatically publish, integrate and execute applications across computational platforms. Boutiques applications are installed through software containers described in a rich and flexible JSON language. A set of core tools facilitate the construction, validation, import, execution, and publishing of applications. Boutiques is currently supported by several distinct virtual research platforms, and it has been used to describe dozens of applications in the neuroinformatics domain. We expect Boutiques to improve the quality of application integration in computational platforms, to reduce redundancy of effort, to contribute to computational reproducibility, and to foster Open Science., Comment: 10 pages