Min Chen

. Here we report a comprehensive and high-resolution transcriptomic and spatial cell-type atlas for the whole adult mouse brain. The cell-type atlas was created by combining a single-cell RNA-sequencing (scRNA-seq) dataset of around 7 million cells profiled (approximately 4.0 million cells passing quality control), and a spatial transcriptomic dataset of approximately 4.3 million cells using multiplexed error-robust fluorescence in situ hybridization (MERFISH). The atlas is hierarchically organized into 4 nested levels of classification: 34 classes, 338 subclasses, 1,201 supertypes and 5,322 clusters. We present an online platform, Allen Brain Cell Atlas, to visualize the mouse whole-brain cell-type atlas along with the single-cell RNA-sequencing and MERFISH datasets. We systematically analysed the neuronal and non-neuronal cell types across the brain and identified a high degree of correspondence between transcriptomic identity and spatial specificity for each cell type. The results reveal unique features of cell-type organization in different brain regions-in particular, a dichotomy between the dorsal and ventral parts of the brain. The dorsal part contains relatively fewer yet highly divergent neuronal types, whereas the ventral part contains more numerous neuronal types that are more closely related to each other. Our study also uncovered extraordinary diversity and heterogeneity in neurotransmitter and neuropeptide expression and co-expression patterns in different cell types. Finally, we found that transcription factors are major determinants of cell-type classification and identified a combinatorial transcription factor code that defines cell types across all parts of the brain. The whole mouse brain transcriptomic and spatial cell-type atlas establishes a benchmark reference atlas and a foundational resource for integrative investigations of cellular and circuit function, development and evolution of the mammalian brain.

Considering the problem of novel view synthesis (NVS) from only a set of 2D images, we simplify the training process of Neural Radiance Field (NeRF) on forward-facing scenes by removing the requirement of known or pre-computed camera parameters, including both intrinsics and 6DoF poses. To this end, we propose NeRF$--$, with three contributions: First, we show that the camera parameters can be jointly optimised as learnable parameters with NeRF training, through a photometric reconstruction; Second, to benchmark the camera parameter estimation and the quality of novel view renderings, we introduce a new dataset of path-traced synthetic scenes, termed as Blender Forward-Facing Dataset (BLEFF); Third, we conduct extensive analyses to understand the training behaviours under various camera motions, and show that in most scenarios, the joint optimisation pipeline can recover accurate camera parameters and achieve comparable novel view synthesis quality as those trained with COLMAP pre-computed camera parameters. Our code and data are available at https://nerfmm.active.vision.

In this paper, we present a novel recurrent multi-view stereo network based on long short-term memory (LSTM) with adaptive aggregation, namely AA-RMVSNet. We firstly introduce an intra-view aggregation module to adaptively extract image features by using context-aware convolution and multi-scale aggregation, which efficiently improves the performance on challenging regions, such as thin objects and large low-textured surfaces. To overcome the difficulty of varying occlusion in complex scenes, we propose an interview cost volume aggregation module for adaptive pixel-wise view aggregation, which is able to preserve better-matched pairs among all views. The two proposed adaptive aggregation modules are lightweight, effective and complementary regarding improving the accuracy and completeness of 3D reconstruction. Instead of conventional 3D CNNs, we utilize a hybrid network with recurrent structure for cost volume regularization, which allows high-resolution reconstruction and finer hypothetical plane sweep. The proposed network is trained end-to-end and achieves excellent performance on various datasets. It ranks 1 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">st</sup> among all submissions on Tanks and Temples benchmark and achieves competitive results on DTU dataset, which exhibits strong generalizability and robustness. Implementation of our method is available at https://github.com/QT-Zhu/AA-RMVSNet.

The mammalian brain is composed of millions to billions of cells that are organized into numerous cell types with specific spatial distribution patterns and structural and functional properties. An essential step towards understanding brain function is to obtain a parts list, i.e., a catalog of cell types, of the brain. Here, we report a comprehensive and high-resolution transcriptomic and spatial cell type atlas for the whole adult mouse brain. The cell type atlas was created based on the combination of two single-cell-level, whole-brain-scale datasets: a single-cell RNA-sequencing (scRNA-seq) dataset of ~7 million cells profiled, and a spatially resolved transcriptomic dataset of ~4.3 million cells using MERFISH. The atlas is hierarchically organized into five nested levels of classification: 7 divisions, 32 classes, 306 subclasses, 1,045 supertypes and 5,200 clusters. We systematically analyzed the neuronal, non-neuronal, and immature neuronal cell types across the brain and identified a high degree of correspondence between transcriptomic identity and spatial specificity for each cell type. The results reveal unique features of cell type organization in different brain regions, in particular, a dichotomy between the dorsal and ventral parts of the brain: the dorsal part contains relatively fewer yet highly divergent neuronal types, whereas the ventral part contains more numerous neuronal types that are more closely related to each other. We also systematically characterized cell-type specific expression of neurotransmitters, neuropeptides, and transcription factors. The study uncovered extraordinary diversity and heterogeneity in neurotransmitter and neuropeptide expression and co-expression patterns in different cell types across the brain, suggesting they mediate a myriad of modes of intercellular communications. Finally, we found that transcription factors are major determinants of cell type classification in the adult mouse brain and identified a combinatorial transcription factor code that defines cell types across all parts of the brain. The whole-mouse-brain transcriptomic and spatial cell type atlas establishes a benchmark reference atlas and a foundational resource for deep and integrative investigations of cell type and circuit function, development, and evolution of the mammalian brain.

Significance Anterograde axonal transport supplies organelles and protein complexes throughout axonal processes to support neuronal morphology and function. It has been observed that reduced anterograde axonal transport is associated with neuronal diseases. In contrast, here we show that particular disease-associated mutations in KIF1A, an anterograde axonal motor for synaptic vesicle precursors, induce hyperactivation of KIF1A motor activity and increased axonal transport of synaptic vesicle precursors. Our results advance the existing knowledge of the regulation of motor proteins in axonal transport and provide insight into the cell biology of motor neuron diseases.