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We are now in the era of millimeter-scale electron microscopy (EM) volumes collected at nanometer resolution (Shapson-Coe et al., 2021; Consortium et al., 2021). Dense reconstruction of cellular compartments in these EM volumes has been enabled by recent advances in Machine Learning (ML) (Lee et al., 2017; Wu et al., 2021; Lu et al., 2021; Macrina et al., 2021). Automated segmentation methods can now yield exceptionally accurate reconstructions of cells, but despite this accuracy, laborious post-hoc proofreading is still required to generate large connectomes free of merge and split errors. The elaborate 3-D meshes of neurons produced by these segmentations contain detailed morphological information, from the diameter, shape, and branching patterns of axons and dendrites, down to the fine-scale structure of dendritic spines. However, extracting information about these features can require substantial effort to piece together existing tools into custom workflows. Building on existing open-source software for mesh manipulation, here we present “NEURD”, a software package that decomposes each meshed neuron into a compact and extensively-annotated graph representation. With these feature-rich graphs, we implement workflows for state of the art automated post-hoc proofreading of merge errors, cell classification, spine detection, axon-dendritic proximities, and other features that can enable many downstream analyses of neural morphology and connectivity. NEURD can make these new massive and complex datasets more accessible to neuroscience researchers focused on a variety of scientific questions.

To understand how the neocortex underlies our ability to perceive, think, and act, it is important to study the relationship between circuit connectivity and function. Previous research has shown that excitatory neurons in layer 2/3 of the primary visual cortex of mice with similar response properties are more likely to form connections. However, technical challenges of combining synaptic connectivity and functional measurements have limited these studies to few, highly local connections. Utilizing the millimeter scale and nanometer resolution of the MICrONS dataset, we studied the connectivity-function relationship in excitatory neurons of the mouse visual cortex across interlaminar and interarea projections, assessing connection selectivity at the coarse axon trajectory and fine synaptic formation levels. A digital twin model of this mouse, that accurately predicted responses to arbitrary video stimuli, enabled a comprehensive characterization of the function of neurons. We found that neurons with highly correlated responses to natural videos tended to be connected with each other, not only within the same cortical area but also across multiple layers and visual areas, including feedforward and feedback connections, whereas we did not find that orientation preference predicted connectivity. The digital twin model separated each neuron’s tuning into a feature component (what the neuron responds to) and a spatial component (where the neuron’s receptive field is located). We show that the feature, but not the spatial component, predicted which neurons were connected at the fine synaptic scale. Together, our results demonstrate the “like-to-like” connectivity rule generalizes to multiple connection types, and the rich MICrONS dataset is suitable to further refine a mechanistic understanding of circuit structure and function.

Due to advances in automated image acquisition and analysis, whole-brain connectomes with 100,000 or more neurons are on the horizon. Proofreading of whole-brain automated reconstructions will require many person-years of effort, due to the huge volumes of data involved. Here we present FlyWire, an online community for proofreading neural circuits in a Drosophila melanogaster brain and explain how its computational and social structures are organized to scale up to whole-brain connectomics. Browser-based three-dimensional interactive segmentation by collaborative editing of a spatially chunked supervoxel graph makes it possible to distribute proofreading to individuals located virtually anywhere in the world. Information in the edit history is programmatically accessible for a variety of uses such as estimating proofreading accuracy or building incentive systems. An open community accelerates proofreading by recruiting more participants and accelerates scientific discovery by requiring information sharing. We demonstrate how FlyWire enables circuit analysis by reconstructing and analyzing the connectome of mechanosensory neurons.

Neurons in the neocortex exhibit astonishing morphological diversity which is critical for properly wiring neural circuits and giving neurons their functional properties. The extent to which the morphological diversity of excitatory neurons forms a continuum or is built from distinct clusters of cell types remains an open question. Here we took a data-driven approach using graph-based machine learning methods to obtain a low-dimensional morphological “bar code” describing more than 30,000 excitatory neurons in mouse visual areas V1, AL and RL that were reconstructed from a millimeter scale serial-section electron microscopy volume. We found a set of principles that captured the morphological diversity of the dendrites of excitatory neurons. First, their morphologies varied with respect to three major axes: soma depth, total apical and basal skeletal length. Second, neurons in layer 2/3 showed a strong trend of a decreasing width of their dendritic arbor and a smaller tuft with increasing cortical depth. Third, in layer 4, atufted neurons were primarily located in the primary visual cortex, while tufted neurons were more abundant in higher visual areas. Fourth, we discovered layer 4 neurons in V1 on the border to layer 5 which showed a tendency towards avoiding deeper layers with their dendrites. In summary, excitatory neurons exhibited a substantial degree of dendritic morphological variation, both within and across cortical layers, but this variation mostly formed a continuum, with only a few notable exceptions in deeper layers.

Neurons in the developing brain undergo extensive structural refinement as nascent circuits adopt their mature form. This physical transformation of neurons is facilitated by the engulfment and degradation of axonal branches and synapses by surrounding glial cells, including microglia and astrocytes. However, the small size of phagocytic organelles and the complex, highly ramified morphology of glia have made it difficult to define the contribution of these and other glial cell types to this crucial process. Here, we used large-scale, serial section transmission electron microscopy (TEM) with computational volume segmentation to reconstruct the complete 3D morphologies of distinct glial types in the mouse visual cortex, providing unprecedented resolution of their morphology and composition. Unexpectedly, we discovered that the fine processes of oligodendrocyte precursor cells (OPCs), a population of abundant, highly dynamic glial progenitors, frequently surrounded small branches of axons. Numerous phagosomes and phagolysosomes (PLs) containing fragments of axons and vesicular structures were present inside their processes, suggesting that OPCs engage in axon pruning. Single-nucleus RNA sequencing from the developing mouse cortex revealed that OPCs express key phagocytic genes at this stage, as well as neuronal transcripts, consistent with active axon engulfment. Although microglia are thought to be responsible for the majority of synaptic pruning and structural refinement, PLs were ten times more abundant in OPCs than in microglia at this stage, and these structures were markedly less abundant in newly generated oligodendrocytes, suggesting that OPCs contribute substantially to the refinement of neuronal circuits during cortical development.

Mammalian neocortex contains a highly diverse set of cell types. These types have been mapped systematically using a variety of molecular, electrophysiological and morphological approaches. Each modality offers new perspectives on the variation of biological processes underlying cell type specialization. While many morphological surveys focus on branching patterns of individual cells, fewer have been devoted to sub-cellular structure of cells. Electron microscopy (EM) provides dense ultrastructural examination and an unbiased perspective into the subcellular organization of brain cells, including their synaptic connectivity and nanometer scale morphology. Here we present the first systematic survey of the somatic region of nearly 100,000 cortical cells, using quantitative features obtained from EM. This analysis demonstrates a surprising sufficiency of the perisomatic region to recapitulate many known aspects of cortical organization, while also revealing novel relationships. Parameters of cell size, nuclear infolding and somatic synaptic innervation co-vary with distinct patterns across depth and between types. Further, we describe how these subcellular features can be used to create highly accurate predictions of cell-types across large scale EM datasets. More generally, our results suggest that the shifts in cellular physiology and molecular programming seen across cell types accompany profound differences in the fine-scale structure of cells.

To evaluate the feasibility and safety of percutaneous transluminal forceps biopsy (PTFB) with an adjustable curved sheath in patients with obstructive jaundice.Forty-two patients who underwent PTFB with an adjustable curved sheath were analyzed retrospectively. Sensitivity, specificity, negative predictive value (NPV), positive predictive value (PPV) and accuracy were calculated for all populations and in different situations. Technical success and safety were evaluated.The technical success rate was 100%. Thirty-five of 42 cases were diagnosed malignant diseases, the sensitivity of PTFB with an adjustable curved sheath was 74.29% (26/35), the specificity was 100%, the positive predictive value was 100%, the negative predictive value was 43.75% (7/16), and the accuracy rate was 78.57% (33/42). There was a better sensitivity for bile duct malignancies when compared with non-bile duct malignancies (PTFB with an adjustable curved sheath is an effective and safe technique, without being limited by approaches and obstruction sites.

The purpose of this prospective randomized study was to compare the nosocomial biliary tract infection rate of biliary stent implantation with a biliary stent loaded with radioactive 125 I seeds (radioactive biliary stent, RBS) and conventional biliary stent (CBS); additionally, to preliminary discuss the causes of postoperative cholangitis. Moreover, the results will provide clinical evidence for the prevention of postoperative biliary tract infection.We prospectively analyzed the nosocomial infection rate of the distal malignant biliary obstruction (MBO) treatment by stent implantation with RBS and CBS. All MBO patients who initially visited our tertiary hospital between July 2015 and December 2019 (n= 196) were evaluated, enrolled, and randomly divided into 2 groups, RBS (n=97) and CBS (n=99) group. χ 2 test was used to evaluate the categorical data, and t test was used to evaluate the numerical data.Our analysis of the study showed the incidence of postoperative infections of a biliary tract of the RBS group (23.7%) was significantly higher than the CBS group (11.1%). The difference was statistically significant (χ 2 =5.425, P =0.020). Our study also showed the most common pathogenic bacteria after surgery was Escherichia coli (26.5%).Treatment for distal MBO with biliary stent loaded with radioactive 125 I seeds had a higher nosocomial infection rate, and the most common pathogenic bacteria was E coli. , Supplemental Digital Content 1, http://links.lww.com/sle/A350.

Background The aim of the study is to analyze the effect of multiple punctures in computed tomography (CT)-guided microcoil localization of pulmonary nodules with other risk factors for common complications. Methods Consecutive patients who underwent CT-guided microcoil localization and subsequent video-assisted thoracoscopic surgery (VATS) between January 2020 and February 2021 were enrolled. Nodules successfully located after only one puncture were defined as the single puncture group, and nodules requiring two or more punctures were defined as the multiple puncture group. Binary logistic regression analysis was performed to assess the relationship between the number of punctures and pneumothorax and intrapulmonary hemorrhage. Results A total of 121 patients were included. There were 98 (68.1%) pulmonary nodules in the single puncture group compared with 46 (31.9%) nodules in the multiple puncture group. The frequencies of pneumothorax and intrapulmonary hemorrhage were higher in the multiple puncture group than in the single puncture group (p = 0.019 and Conclusion Multiple punctures resulted in an increased incidence of pneumothorax and intrapulmonary hemorrhage compared with single puncture during CT-guided microcoil localization of pulmonary nodules and were independently associated with both pneumothorax and intrapulmonary hemorrhage.

Objective To investigate and summarize the effectiveness and safety of CT guided microcoil localization before video-assisted thoracic surgery (VATS) for the removal of ground glass opacity (GGO).Method 147 patients with GGO who were treated in our hospital from January 2019 to February 2021 were retrospectively analyzed. They were divided into two groups according to the final position of the end of the microcoil, intracavity group (n=78) and extracavity group (n=69). Comparison of the two groups of patients with puncture complications, and the influence of the end position of the coil for VATS.Results The proportion of supine and prone position in the intracavity group was significantly higher than that in the extracavity group (82.1% vs. 66.7%, P0.05). The time of VATS and the rate of conversion to thoracotomy in the intracavity group were significantly lower than those in the extracavity group (103.4±21.0min vs. 112.2±17.3min, 0% vs. 5.8%, PConclusion CT-guided placement of the microcoil was a very practical, simple and convenient localization method before VATS with high success rate and few complications, further more, it was a better method to place the end of the coil in the pleural cavity because of the lower complication rate, shorter VATS time and lower rate of thoracotomy conversion.

Benefiting from the rapid development of electron microscopy imaging and deep learning technologies, an increasing number of brain image datasets with segmentation and synapse detection are published. Most of the automated segmentation methods label voxels rather than producing neuron skeletons directly. A further skeletonization step is necessary for quantitative morphological analysis. Currently, several tools are published for skeletonization as well as morphological and synaptic connectivity analysis using different computer languages and environments. Recently the Julia programming language, notable for elegant syntax and high performance, has gained rapid adoption in the scientific computing community. Here, we present a Julia package, called RealNeuralNetworks.jl, for efficient sparse skeletonization, morphological analysis, and synaptic connectivity analysis. Based on a large-scale Zebrafish segmentation dataset, we illustrate the software features by performing distributed skeletonization in Google Cloud, clustering the neurons using the NBLAST algorithm, combining morphological similarity and synaptic connectivity to study their relationship. We demonstrate that RealNeuralNetworks.jl is suitable for use in terabyte-scale electron microscopy image segmentation datasets.

Inhibitory neurons in mammalian cortex exhibit diverse physiological, morphological, molecular, and connectivity signatures. While considerable work has measured the average connectivity of several interneuron classes, there remains a fundamental lack of understanding of the connectivity distribution of distinct inhibitory cell types with synaptic resolution, how it relates to properties of target cells, and how it affects function. Here, we used large-scale electron microscopy and functional imaging to address these questions for chandelier cells in layer 2/3 of the mouse visual cortex. With dense reconstructions from electron microscopy, we mapped the complete chandelier input onto 153 pyramidal neurons. We found that synapse number is highly variable across the population and is correlated with several structural features of the target neuron. This variability in the number of axo-axonic ChC synapses is higher than the variability seen in perisomatic inhibition. Biophysical simulations show that the observed pattern of axo-axonic inhibition is particularly effective in controlling excitatory output when excitation and inhibition are co-active. Finally, we measured chandelier cell activity in awake animals using a cell-type-specific calcium imaging approach and saw highly correlated activity across chandelier cells. In the same experiments, in vivo chandelier population activity correlated with pupil dilation, a proxy for arousal. Together, these results suggest that chandelier cells provide a circuit-wide signal whose strength is adjusted relative to the properties of target neurons.

We reconstructed all cell nuclei in a 3D image of a Drosophila brain acquired by serial section electron microscopy (EM). The total number of nuclei is approximately 133,000, at least 87% of which belong to neurons. Neuronal nuclei vary from several hundred down to roughly 5 cubic micrometers. Glial nuclei can be even smaller. The optic lobes contain more than two times the number of cells than the central brain. Our nuclear reconstruction serves as a spatial map and index to the cells in a Drosophila brain.

Flame retardants (FRs) often reduce the mechanical properties of polymer materials, and FR/microcellular polyurethane elastomer (MPUE) composite materials have not been systemically studied. Hence, we conducted this study on FR/MPUE composites by using multiple liquid FRs and/or expandable graphite (EG). Compared with liquid flame retardants, the LOI of an expandable graphite/dimethyl methylphosphonate (EG/DMMP) (3:1) combination was significantly increased (~36.1%), and the vertical combustion grade reached V-0 without a dripping phenomenon. However, the corresponding tensile strength was decreased by 17.5%. With the incorporation of EG alone, although the corresponding LOI was not a match with that of DMMP/EG, there was no droplet phenomenon. In addition, even with 15 wt% of EG, there was no significant decline in the tensile strength. Cone calorimeter test results showed that PHRR, THR, PSPR, and TSR were significantly reduced, compared to the neat MPUE, when the EG content surpassed 10 wt%. The combustion process became more stable and thus the fire risk was highly reduced. It was found that flame retardancy and mechanical properties could be well balanced by adding EG alone. Our proposed strategy for synthesizing FR/MPUE composites with excellent flame retardancy and mechanical properties was easy, effective, low-cost and universal, which could have great practical significance in expanding the potential application fields of MPUEs.