Gossamer: Scaling Image Processing and Reconstruction to Whole Brains.

Neuronal reconstruction-a process that transforms image volumes into 3D geometries and skeletons of cells- bottlenecks the study of brain function, connectomics and pathology. Domain scientists need exact and complete segmentations to study subtle topological differences. Existing methods are diskbound, dense-access, coupled, single-threaded, algorithmically unscalable and require manual cropping of small windows and proofreading of skeletons due to low topological accuracy. Designing a data-intensive parallel solution suited to a neurons' shape, topology and far-ranging connectivity is particularly challenging due to I/O and load-balance, yet by abstracting these vision tasks into strategically ordered specializations of search, we progressively lower memory by 4 orders of magnitude. This enables 1 mouse brain to be fully processed in-memory on a single server, at 67× the scale with 870× less memory while having 78% higher automated yield than APP2, the previous state of the art in performant reconstruction.

Dendritome Mapping Unveils Spatial Organization of Striatal D1/D2-Neuron Morphology.

Morphology is a cardinal feature of a neuron that mediates its functions, but profiling neuronal morphologies at scale remains a formidable challenge. Here we describe a generalizable pipeline for large-scale brainwide study of dendritic morphology of genetically-defined single neurons in the mouse brain. We generated a dataset of 3,762 3D-reconstructed and reference-atlas mapped striatal D1- and D2- medium spiny neurons (MSNs). Integrative morphometric analyses reveal distinct impacts of anatomical locations and D1/D2 genetic types on MSN morphologies. To analyze striatal regional features of MSN dendrites without prior anatomical constraints, we assigned MSNs to a lattice of cubic boxes in the reference brain atlas, and summarized morphometric representation ("eigen-morph") for each box and clustered boxes with shared morphometry. This analysis reveals 6 modules with characteristic dendritic features and spanning contiguous striatal territories, each receiving distinct corticostriatal inputs. Finally, we found aging confers robust dendritic length and branching defects in MSNs, while Huntington's disease (HD) mice exhibit selective length-related defects. Together, our study demonstrates a systems-biology approach to profile dendritic morphology of genetically-defined single-neurons; and defines novel striatal D1/D2-MSN morphological territories and aging- or HD-associated pathologies.

Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems.

Methods for highly multiplexed RNA imaging are limited in spatial resolution and thus in their ability to localize transcripts to nanoscale and subcellular compartments. We adapt expansion microscopy, which physically expands biological specimens, for long-read untargeted and targeted in situ RNA sequencing. We applied untargeted expansion sequencing (ExSeq) to the mouse brain, which yielded the readout of thousands of genes, including splice variants. Targeted ExSeq yielded nanoscale-resolution maps of RNAs throughout dendrites and spines in the neurons of the mouse hippocampus, revealing patterns across multiple cell types, layer-specific cell types across the mouse visual cortex, and the organization and position-dependent states of tumor and immune cells in a human metastatic breast cancer biopsy. Thus, ExSeq enables highly multiplexed mapping of RNAs from nanoscale to system scale.

Psychosocial Results from a Phase I Trial of a Nonsurgical Circumcision Device for Adult Men in Zimbabwe.

Male circumcision (MC), an effective HIV prevention tool, has been added to Zimbabwe's Ministry of Health and Child Care HIV/AIDS Prevention Program. A Phase I safety trial of a nonsurgical male circumcision device was conducted and extensive psychosocial variables were assessed. Fifty-three men (18 and older) were recruited for the device procedure; 13 follow-up clinical visits were completed. Interviews conducted three times (before the procedure, at 2 weeks and 90 days post-procedure) assessed: Satisfaction; expectations; actual experience; activities of daily living; sexual behavior; and HIV risk perception. Using the Integrated Behavioral Model, attitudes towards MC, sex, and condoms, and sources of social influence and support were also assessed. Men (mean age 32.5, range 18-50; mean years of education = 13.6; 55% employed) were satisfied with device circumcision results. Men understand that MC is only partially protective against HIV acquisition. Most (94.7%) agreed that they will continue to use condoms to protect themselves from HIV. Pain ratings were surprisingly negative for a procedure billed as painless. Men talked to many social networks members about their MC experience; post-procedure (mean of 14 individuals). Minimal impact on activities of daily living and absenteeism indicate possible cost savings of device circumcisions. Spontaneous erections occurred frequently post-procedure. The results had important implications for changes in the pre-procedure clinical counseling protocol. Clear-cut counseling to manage pain and erection expectations should result in improved psychosocial outcomes in future roll-out of device circumcisions. Men's expectations must be managed through evidence-based counseling, as they share their experiences broadly among their social networks.