Human hypothalamus is central to basic physiological functions and its dysfunction is associated with many diseases, yet its spatial cellular and molecular architecture remains poorly understood. Here we present a comprehensive 3D atlas of the adult human hypothalamus aligned to magnetic resonance imaging (MRI) data, integrating spatial transcriptomics, single-nucleus RNA sequencing, and histological analysis. Cross-species comparisons identified homologous regions and subregions between human and mouse hypothalamus. We found that adult human hypothalamus maintained a conserved spatial pattern of transcription factors along the anteroposterior axis established during early development. Furthermore, we uncovered a more segregated neuronal organization in human hypothalamus than mouse and distinctive human features in various hypothalamic nuclei. Finally, we identified the disease landscape in human hypothalamus. Together, our atlas revealed the spatial cellular and molecular organization of the human hypothalamus, helping to bridge experimental animal studies and human clinical investigation.

Abstract The teleost pineal gland is an eye-like photoreceptive organ with a central role in the circadian clock system, primarily through its melatonin-producing photoreceptor cells. However, the functional molecular interactions between pineal photoreceptors, accessory cells predicted to support photoreceptor function, and projecting neurons remain incompletely understood. Here, we integrated single-cell zebrafish pineal transcriptomes with bulk circadian and light-response pineal transcriptomes. Combined analysis of two single-cell datasets identified novel photoreceptor and neuronal subtypes, including parietopsin -expressing cone-like cells and neurons expressing markers of neuronal maturation. Integration with the light-response dataset revealed light inhibition of photoreceptor opsin genes. Integration with circadian transcriptomes from wildtype fish and fish expressing the clock-disrupting dominant-negative CLOCK (ΔCLK) in pineal photoreceptors revealed cell-type-specific rhythmicity. Despite comparable expression of ΔCLK, photoreceptor subtypes differed in sensitivity to rhythm disruption, with rod-like cells (rods) most severely affected. In neurons, despite the absence of ΔCLK expression, rhythm disruption was comparable to that of rods. Moreover, rhythmic neuronal markers and rhythmic photoreceptor markers exhibited a similar circadian pattern, peaking mainly during the early night. These observations suggest that clock function in neurons depend on photoreceptor output. In contrast, accessory cell rhythmic markers were relatively resistant to ΔCLK disruption and peaked predominantly around subjective dawn, consistent with partially autonomous clock function. To facilitate comparative analysis of gene expression, rhythmicity and light responsiveness across pineal cell types, we developed the Zebrafish Pineal Transcriptomics Viewer. Our findings reveal a temporally structured and functionally heterogeneous organization of the zebrafish pineal gland.

The suprachiasmatic nucleus (SCN) is considered the master pacemaker of the circadian clock in mammals, but our current knowledge of the SCN is mostly based on rodent studies. Here, we report a comprehensive molecular and cellular atlas for the adult human SCN by spatial transcriptomics, single-nucleus RNA sequencing, and deep-learning-based histological analysis. We identified seven human SCN neuron subtypes with specific transcriptomes and spatial distributions. Comparison of humans, mice, and non-human primates revealed the conserved functional segregation within the SCN regulated by LIM homeobox 1 (LHX1) and RAR-related orphan receptor B (RORB). Furthermore, our results suggested that the human SCN has undergone marked reorganization of its neuropeptide signaling network. Finally, integrative analysis of human SCN transcriptomes and genome-wide association studies (GWASs) identified arginine vasopressin (AVP)/neuromedin S (NMS) subtype as the potential neuronal correlate for morningness chronotype. Thus, our spatial and single-cell transcriptomic atlas of the human SCN provided a basis for the understanding of neural and molecular mechanisms of the human circadian clock.

The hypothalamus coordinately regulates physiological homeostasis and innate behaviors, yet the detailed arrangement of hypothalamic axons remains unclear. Here we mapped the whole-brain projections of over 7,000 hypothalamic neurons expressing distinct neuropeptides in male mice, identifying 2 main classes and 31 types using single-neuron projectome analysis. These classes/types exhibited regionally biased soma distribution and specific neuropeptide enrichment. Notably, many projectome types extended long-range axon collaterals to distinct brain regions, allowing single axons to co-regulate multiple targets. We uncovered topographic organization of certain peptidergic axons at specific targets, along with diverse single-neuron projectome patterns in Orexin, Agrp and Pomc populations. Furthermore, hypothalamic peptidergic neurons showed correlated innervation of subdomains in the periaqueductal gray and organized into modular subnetworks within the hypothalamus, providing a structural basis for coordinated outputs. This dataset highlights the complexity of hypothalamic axonal projections and lays a foundation for future investigation of the circuit mechanisms underlying hypothalamic functions.

The mammalian cortex orchestrates sensory processing, motor control, and cognition through a complex neural network, yet the organization principles governing single-neuron connectivity and its relationship with transcriptome and neuron activity remain elusive. Here, we reconstructed the projectomes of nearly 20,000 neurons in the whole mouse cortex, identifying 346 projection-defined subtypes with region- and layer-specific distributions. Our analysis uncovered seven cortico-cortical modules with submodular organization, high-resolution cortical hierarchy, and diverse terminal arborization patterns of single neurons refining the traditional feedforward/feedback model. Furthermore, we revealed cortico-subcortical projections, including multiple hyper-direct cortico-basal ganglia pathways, and constructed the detailed topographic maps between cortical neurons and their subcortical target regions. Finally, we showed that our fine-grained cortico-cortical connectivity map is closely related to the cortex-wide Ca2+ activity, electrical neuronal activity, and gene expression. Together, our multimodal analysis provides a foundational framework for understanding the cortical neural network in the mouse brain.

Cortical expansion endows advanced cognitive functions in primates, and whole-brain single-neuron projection analysis helps to elucidate underlying neural circuit mechanisms. Here, we reconstructed 2,231 single-neuron projectomes for the macaque prefrontal cortex (PFC) and identified 32 projectome-based subtypes of intra-telencephalic, pyramidal-tract, and cortico-thalamic neurons. Each subtype exhibited distinct topography in their soma distribution within the PFC, a characteristic pattern of axon targeting, and subregion-specific patchy terminal arborization in the targeted area, with putative functions annotated. Furthermore, we identified a subdomain connectivity network and extensive local axons within the PFC. Compared with those in mice, macaque PFC projectomes exhibited a similar topographic gradient of terminal arborization at the targeted regions but much higher target specificity, fewer collaterals, and smaller brain size-normalized arbors. Thus, whole-brain single-axon macaque projectomes revealed highly refined axon targeting and arborization, providing key insights into the structural basis for complex brain functions in primates.

Deciphering patterns of connectivity between neurons in the brain is a critical step toward understanding brain function. Imaging-based neuroanatomical tracing identifies area-to-area or sparse neuron-to-neuron connectivity patterns, but with limited throughput. Barcode-based connectomics maps large numbers of single-neuron projections, but remains a challenge for jointly analyzing single-cell transcriptomics. Here, we established a rAAV2-retro barcode-based multiplexed tracing method that simultaneously characterizes the projectome and transcriptome at the single neuron level. We uncovered dedicated and collateral projection patterns of ventromedial prefrontal cortex (vmPFC) neurons to five downstream targets and found that projection-defined vmPFC neurons are molecularly heterogeneous. We identified transcriptional signatures of projection-specific vmPFC neurons, and verified Pou3f1 as a marker gene enriched in neurons projecting to the lateral hypothalamus, denoting a distinct subset with collateral projections to both dorsomedial striatum and lateral hypothalamus. In summary, we have developed a new multiplexed technique whose paired connectome and gene expression data can help reveal organizational principles that form neural circuits and process information.

Oxytocin (OXT) plays important roles in autonomic control and behavioral modulation. However, it is unknown how the projection patterns of OXT neurons align with underlying physiological functions. Here, we present the reconstructed single-neuron, whole-brain projectomes of 264 OXT neurons of the mouse paraventricular hypothalamic nucleus (PVH) at submicron resolution. These neurons hierarchically clustered into two groups, with distinct morphological and transcriptional characteristics and mutually exclusive projection patterns. Cluster 1 (177 neurons) axons terminated exclusively in the median eminence (ME) and have few collaterals terminating within hypothalamic regions. By contrast, cluster 2 (87 neurons) sent wide-spread axons to multiple brain regions, but excluding ME. Dendritic arbors of OXT neurons also extended outside of the PVH, suggesting capability to sense signals and modulate target regions. These single-neuron resolution observations reveal distinct OXT subpopulations, provide comprehensive analysis of their morphology, and lay the structural foundation for better understanding the functional heterogeneity of OXT neurons.

Located dorsally underneath a thin translucent skull in many teleosts, the pineal gland is a photoreceptive organ known as a key element of the circadian clock system. Nevertheless, the presence of additional routes of photoreception presents a challenge in determining its specific roles in regulating photic-related behavior. Here, we show the importance of the pineal gland in mediating a prolonged motor response of zebrafish larvae to sudden darkness, both as a photodetector and as a circadian pacemaker. This was evident by a reduced motor response of Bsx-deficient larvae, lacking a pineal gland, to sudden darkness. Moreover, the typical daily rhythm of the intensity of this response was lost in the pineal-less larvae. In contrast, motor response to a sudden increase in illumination was unaffected. Furthermore, we show that the pineal-mediated behavioral response to darkness requires two elements: the photoreceptor cells and the projecting neurons. Dark response was impaired in larvae whose pineal photoreceptor cells were genetically ablated and in larvae whose pineal projecting neurons had undergone laser-axotomy. This study thus establishes the pineal gland as a mediator of dark-dependent behavior and reveals underlying cellular components involved in transducing information about darkness to the brain.

The suprachiasmatic nucleus (SCN) encodes time of day through changes in daily firing; however, the molecular mechanisms by which the SCN times behavior are not fully understood. To identify factors that could encode day/night differences in activity, we combine patch-clamp recordings and single-cell sequencing of individual SCN neurons in mice. We identify PiT2, a phosphate transporter, as being upregulated in a population of Vip+Nms+ SCN neurons at night. Although nocturnal and typically showing a peak of activity at lights off, mice lacking PiT2 (PiT2-/-) do not reach the activity level seen in wild-type mice during the light/dark transition. PiT2 loss leads to increased SCN neuronal firing and broad changes in SCN protein phosphorylation. PiT2-/- mice display a deficit in seasonal entrainment when moving from a simulated short summer to longer winter nights. This suggests that PiT2 is responsible for timing activity and is a driver of SCN plasticity allowing seasonal entrainment.

Mapping single-neuron projections is essential for understanding brain-wide connectivity and diverse functions of the hippocampus (HIP). Here, we reconstructed 10,100 single-neuron projectomes of mouse HIP and classified 43 projectome subtypes with distinct projection patterns. The number of projection targets and axon-tip distribution depended on the soma location along HIP longitudinal and transverse axes. Many projectome subtypes were enriched in specific HIP subdomains defined by spatial transcriptomic profiles. Furthermore, we delineated comprehensive wiring diagrams for HIP neurons projecting exclusively within the HIP formation (HPF) and for those projecting to both intra- and extra-HPF targets. Bihemispheric projecting neurons generally projected to one pair of homologous targets with ipsilateral preference. These organization principles of single-neuron projectomes provide a structural basis for understanding the function of HIP neurons.

Whole-brain analysis of single-neuron morphology is crucial for unraveling the complex structure of the brain. However, large-scale neuron reconstruction from terabyte and even petabyte data of mammalian brains generated by state-of-the-art light microscopy is a daunting task. Here, we developed ‘Gapr’ (Gapr accelerates projectome reconstruction) that streamlines deep learning-based automatic reconstruction, ‘automatic proofreading’ that reduces human workloads at high-confidence sites, and high-throughput collaborative proofreading by crowd users through the Internet. Furthermore, Gapr offers a seamless user interface that ensures high proofreading speed per annotator, on-demand conversion for handling large datasets, flexible workflows tailored to diverse datasets and rigorous error tracking for quality control. Finally, we demonstrated Gapr’s efficacy by reconstructing over 4,000 neurons in mouse brains, revealing the morphological diversity in cortical interneurons and hypothalamic neurons. Here, we present Gapr as a solution for large-scale single-neuron reconstruction projects. Gapr is an efficient platform for reconstructing neurons in large-scale light microscopy datasets. It enables various proofreading modes as well as collaboration among many annotators.

The morphology and spatial distribution of axon arbors and boutons are crucial for neuron presynaptic functions. However, the principles governing their whole-brain organization at the single-neuron level remain unclear. We developed a machine-learning method to separate axon arbors from passing axons in single neuron reconstruction from fluorescence micro-optical sectioning tomography imaging data and obtained 62,374 axon arbors that displayed distinct morphology, spatial patterns, and scaling laws dependent on neuron types and targeted brain areas. Focusing on the axon arbors in the thalamus and cortex, we revealed the segregated spatial distributions and distinct morphology but shared topographic gradients between feedforward and feedback projections. Furthermore, we uncovered an association between arbor complexity and microglia density. Finally, we found that the boutons on terminal arbors show branch-specific clustering with a log-normal distribution that again differed between feedforward and feedback terminal arbors. Together, our study revealed distinct presynaptic structural organizations underlying diverse functional innervation of single projection neurons.

The structures of dendrites and axons form the basis for the connectivity of neural network, but their precise relationship at single-neuron level remains unclear. Here we report the complete dendrite and axon morphology of nearly 2,000 neurons in mouse prefrontal cortex (PFC). We identified morphological variations of somata, dendrites and axons across laminar layers and PFC subregions and the general rules of somatodendritic scaling with cytoarchitecture. We uncovered 24 morphologically distinguishable dendrite subtypes in 1,515 pyramidal projection neurons and 405 atypical pyramidal projection neurons and spiny stellate neurons with unique axon projection patterns. Furthermore, correspondence analysis among dendrites, local axons and long-range axons revealed coherent morphological changes associated with electrophysiological phenotypes. Finally, integrative dendrite–axon analysis uncovered the organization of potential intra-column, inter-hemispheric and inter-column connectivity among projection neuron types in PFC. Together, our study provides a comprehensive structural repertoire for the reconstruction and analysis of PFC neural network.

The suprachiasmatic nucleus (SCN) can generate robust circadian behaviors in mammals under different environments, but the underlying neural mechanisms remained unclear. Here, we showed that the activities of cholecystokinin (CCK) neurons in the mouse SCN preceded the onset of behavioral activities under different photoperiods. CCK-neuron-deficient mice displayed shortened free-running periods, failed to compress their activities under a long photoperiod, and developed rapid splitting or became arrhythmic under constant light. Furthermore, unlike vasoactive intestinal polypeptide (VIP) neurons, CCK neurons are not directly light sensitive, but their activation can elicit phase advance and counter light-induced phase delay mediated by VIP neurons. Under long photoperiods, the impact of CCK neurons on SCN dominates over that of VIP neurons. Finally, we found that the slow-responding CCK neurons control the rate of recovery during jet lag. Together, our results demonstrated that SCN CCK neurons are crucial for the robustness and plasticity of the mammalian circadian clock.

The circadian clock orchestrates a wide variety of physiological and behavioral processes, enabling animals to adapt to daily environmental changes, particularly the day-night cycle. However, the circadian clock's role in the developmental processes remains unclear. Here, we employ the in vivo long-term time-lapse imaging of retinotectal synapses in the optic tectum of larval zebrafish and reveal that synaptogenesis, a fundamental developmental process for neural circuit formation, exhibits circadian rhythm. This rhythmicity arises primarily from the synapse formation rather than elimination and requires the hypocretinergic neural system. Disruption of this synaptogenic rhythm, by impairing either the circadian clock or the hypocretinergic system, affects the arrangement of the retinotectal synapses on axon arbors and the refinement of the postsynaptic tectal neuron's receptive field. Thus, our findings demonstrate that the developmental synaptogenesis is under hypocretin-dependent circadian regulation, suggesting an important role of the circadian clock in neural development.

The hypothalamus plays a vital role in coordinating essential neuroendocrine, autonomic, and somatomotor responses for survival and reproduction. While previous studies have explored population-level projections of hypothalamic neurons, the specific innervation patterns of individual hypothalamic axons remain unclear. To understand the organization of hypothalamic axon projections, we conducted a comprehensive reconstruction of single-cell projectomes from 7,180 mouse hypothalamic neurons expressing specific neuropeptides. Our analysis identified 31 distinct subtypes based on projectome-defined characteristics, with many exhibiting long-range axon collateral projections to multiple brain regions. Notably, these subtypes selectively targeted specific subdomains within downstream areas, either unilaterally or bilaterally. Furthermore, we observed that individual peptidergic neuronal types encompassed multiple projectome-defined subtypes, explaining their diverse functional roles. Additionally, by examining intra-hypothalamic axon projections, we uncovered six modular subnetworks characterized by enriched intramodular connections and distinct preferences for downstream targets. This modular organization of the intra-hypothalamic network likely contributes to the coordinated organization of hypothalamic outputs. In summary, our comprehensive projectome analysis reveals the organizational principles governing hypothalamic axon projections, providing a framework for understanding the neural circuit mechanisms underlying the diverse and coordinated functions of the hypothalamus.

An efficient tool for neurite tracing has been developed that reconstructed the complete axons of 6,357 individual projection neurons in the mouse prefrontal cortex (PFC). The resulting single-neuron projectome analysis revealed comprehensive PFC neuron subtypes, topographic organization of PFC axon projections, modular structure within the PFC and correspondence with single-cell transcriptomes.