Non-homogenous axonal bouton distribution in whole-brain single-cell neuronal networks.

We examined the distribution of pre-synaptic contacts in axons of mouse neurons and constructed whole-brain single-cell neuronal networks using an extensive dataset of 1,891 fully reconstructed neurons. We found that bouton locations were not homogeneous throughout the axon and among brain regions. As our algorithm was able to generate whole-brain single-cell connectivity matrices from full morphology reconstruction datasets, we further found that non-homogeneous bouton locations have a significant impact on network wiring, including degree distribution, triad census, and community structure. By perturbing neuronal morphology, we further explored the link between anatomical details and network topology. In our in silico exploration, we found that dendritic and axonal tree span would have the greatest impact on network wiring, followed by synaptic contact deletion. Our results suggest that neuroanatomical details must be carefully addressed in studies of whole-brain networks at the single-cell level.

Full-Spectrum Neuronal Diversity and Stereotypy through Whole Brain Morphometry.

We conducted a large-scale study of whole-brain morphometry, analyzing 3.7 peta-voxels of mouse brain images at the single-cell resolution, producing one of the largest multi-morphometry databases of mammalian brains to date. We spatially registered 205 mouse brains and associated data from six Brain Initiative Cell Census Network (BICCN) data sources covering three major imaging modalities from five collaborative projects to the Allen Common Coordinate Framework (CCF) atlas, annotated 3D locations of cell bodies of 227,581 neurons, modeled 15,441 dendritic microenvironments, characterized the full morphology of 1,891 neurons along with their axonal motifs, and detected 2.58 million putative synaptic boutons. Our analysis covers six levels of information related to neuronal populations, dendritic microenvironments, single-cell full morphology, sub-neuronal dendritic and axonal arborization, axonal boutons, and structural motifs, along with a quantitative characterization of the diversity and stereotypy of patterns at each level. We identified 16 modules consisting of highly intercorrelated brain regions in 13 functional brain areas corresponding to 314 anatomical regions in CCF. Our analysis revealed the dendritic microenvironment as a powerful method for delineating brain regions of cell types and potential subtypes. We also found that full neuronal morphologies can be categorized into four distinct classes based on spatially tuned morphological features, with substantial cross-areal diversity in apical dendrites, basal dendrites, and axonal arbors, along with quantified stereotypy within cortical, thalamic and striatal regions. The lamination of somas was found to be more effective in differentiating neuron arbors within the cortex. Further analysis of diverging and converging projections of individual neurons in 25 regions throughout the brain reveals branching preferences in the brain-wide and local distributions of axonal boutons. Overall, our study provides a comprehensive description of key anatomical structures of neurons and their types, covering a wide range of scales and features, and contributes to our understanding of neuronal diversity and its function in the mammalian brain.

NRRS: a re-tracing strategy to refine neuron reconstruction.

It is crucial to develop accurate and reliable algorithms for fine reconstruction of neural morphology from whole-brain image datasets. Even though the involvement of human experts in the reconstruction process can help to ensure the quality and accuracy of the reconstructions, automated refinement algorithms are necessary to handle substantial deviations problems of reconstructed branches and bifurcation points from the large-scale and high-dimensional nature of the image data. Our proposed Neuron Reconstruction Refinement Strategy (NRRS) is a novel approach to address the problem of deviation errors in neuron morphology reconstruction. Our method partitions the reconstruction into fixed-size segments and resolves the deviation problems by re-tracing in two steps. We also validate the performance of our method using a synthetic dataset. Our results show that NRRS outperforms existing solutions and can handle most deviation errors. We apply our method to SEU-ALLEN/BICCN dataset containing 1741 complete neuron reconstructions and achieve remarkable improvements in the accuracy of the neuron skeleton representation, the task of radius estimation and axonal bouton detection. Our findings demonstrate the critical role of NRRS in refining neuron morphology reconstruction. Availability and implementation: The proposed refinement method is implemented as a Vaa3D plugin and the source code are available under the repository of vaa3d_tools/hackathon/Levy/refinement. The original fMOST images of mouse brains can be found at the BICCN's Brain Image Library (BIL) (https://www.brainimagelibrary.org). The synthetic dataset is hosted on GitHub (https://github.com/Vaa3D/vaa3d_tools/tree/master/hackathon/Levy/refinement). Supplementary information: Supplementary data are available at Bioinformatics Advances online.

Petabyte-Scale Multi-Morphometry of Single Neurons for Whole Brains.

Recent advances in brain imaging allow producing large amounts of 3-D volumetric data from which morphometry data is reconstructed and measured. Fine detailed structural morphometry of individual neurons, including somata, dendrites, axons, and synaptic connectivity based on digitally reconstructed neurons, is essential for cataloging neuron types and their connectivity. To produce quality morphometry at large scale, it is highly desirable but extremely challenging to efficiently handle petabyte-scale high-resolution whole brain imaging database. Here, we developed a multi-level method to produce high quality somatic, dendritic, axonal, and potential synaptic morphometry, which was made possible by utilizing necessary petabyte hardware and software platform to optimize both the data and workflow management. Our method also boosts data sharing and remote collaborative validation. We highlight a petabyte application dataset involving 62 whole mouse brains, from which we identified 50,233 somata of individual neurons, profiled the dendrites of 11,322 neurons, reconstructed the full 3-D morphology of 1,050 neurons including their dendrites and full axons, and detected 1.9 million putative synaptic sites derived from axonal boutons. Analysis and simulation of these data indicate the promise of this approach for modern large-scale morphology applications.

Image enhancement to leverage the 3D morphological reconstruction of single-cell neurons.

MOTIVATION: To digitally reconstruct the 3D neuron morphologies has long been a major bottleneck in neuroscience. One of the obstacles to automate the procedure is the low signal-background contrast (SBC) and the large dynamic range of signal and background both within and across images. RESULTS: We developed a pipeline to enhance the neurite signal and to suppress the background, with the goal of high SBC and better within- and between-image homogeneity. The performance of the image enhancement was quantitatively verified according to the different figures of merit benchmarking the image quality. In addition, the method could improve the neuron reconstruction in approximately 1/3 of the cases, with very few cases of degrading the reconstruction. This significantly outperformed three other approaches of image enhancement. Moreover, the compression rate was increased five times by average comparing the enhanced to the raw image. All results demonstrated the potential of the proposed method in leveraging the neuroscience by providing better 3D morphological reconstruction and lower cost of data storage and transfer. AVAILABILITY AND IMPLEMENTATION: The study is conducted based on the Vaa3D platform and python 3.7.9. The Vaa3D platform is available on the GitHub (https://github.com/Vaa3D). The source code of the proposed image enhancement as a Vaa3D plugin, the source code to benchmark the image quality and the example image blocks are available under the repository of vaa3d_tools/hackathon/SGuo/imPreProcess. The original fMost images of mouse brains can be found at the BICCN's Brain Image Library (BIL) (https://www.brainimagelibrary.org). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Morphological diversity of single neurons in molecularly defined cell types.

Dendritic and axonal morphology reflects the input and output of neurons and is a defining feature of neuronal types1,2, yet our knowledge of its diversity remains limited. Here, to systematically examine complete single-neuron morphologies on a brain-wide scale, we established a pipeline encompassing sparse labelling, whole-brain imaging, reconstruction, registration and analysis. We fully reconstructed 1,741 neurons from cortex, claustrum, thalamus, striatum and other brain regions in mice. We identified 11 major projection neuron types with distinct morphological features and corresponding transcriptomic identities. Extensive projectional diversity was found within each of these major types, on the basis of which some types were clustered into more refined subtypes. This diversity follows a set of generalizable principles that govern long-range axonal projections at different levels, including molecular correspondence, divergent or convergent projection, axon termination pattern, regional specificity, topography, and individual cell variability. Although clear concordance with transcriptomic profiles is evident at the level of major projection type, fine-grained morphological diversity often does not readily correlate with transcriptomic subtypes derived from unsupervised clustering, highlighting the need for single-cell cross-modality studies. Overall, our study demonstrates the crucial need for quantitative description of complete single-cell anatomy in cell-type classification, as single-cell morphological diversity reveals a plethora of ways in which different cell types and their individual members may contribute to the configuration and function of their respective circuits.

Binocular Encoding in the Damselfly Pre-motor Target Tracking System.

Akin to all damselflies, Calopteryx (family Calopterygidae), commonly known as jewel wings or demoiselles, possess dichoptic (separated) eyes with overlapping visual fields of view. In contrast, many dragonfly species possess holoptic (dorsally fused) eyes with limited binocular overlap. We have here compared the neuronal correlates of target tracking between damselfly and dragonfly sister lineages and linked these changes in visual overlap to pre-motor neural adaptations. Although dragonflies attack prey dorsally, we show that demoiselles attack prey frontally. We identify demoiselle target-selective descending neurons (TSDNs) with matching frontal visual receptive fields, anatomically and functionally homologous to the dorsally positioned dragonfly TSDNs. By manipulating visual input using eyepatches and prisms, we show that moving target information at the pre-motor level depends on binocular summation in demoiselles. Consequently, demoiselles encode directional information in a binocularly fused frame of reference such that information of a target moving toward the midline in the left eye is fused with information of the target moving away from the midline in the right eye. This contrasts with dragonfly TSDNs, where receptive fields possess a sharp midline boundary, confining responses to a single visual hemifield in a sagittal frame of reference (i.e., relative to the midline). Our results indicate that, although TSDNs are conserved across Odonata, their neural inputs, and thus the upstream organization of the target tracking system, differ significantly and match divergence in eye design and predatory strategies. VIDEO ABSTRACT.