The medial amygdala plays a key role in social brain networks supporting affiliation behavior. This whole domain is widely considered a subpallial (GABAergic) amygdalar subdivision, although it is composed of a mixture of cells of different origins, including populations migrated from the hypothalamus, the prethalamic eminence and the neighboring pallial amygdala. Specifically, the ventral part of the medial amygdala has a high percentage of glutamatergic cells. We developed a transcriptomic study (snRNAseq) to examine the pallial versus subpallial ascription of the mouse medial amygdala cells. We detected high molecular similarity between the ventral region of the medial amygdala and the pallial anterior amygdalar radial unit (classical anterior basomedial nucleus, BMA, and anterior cortical nucleus, ACo), in contrast with the GABAergic profile of the posterodorsal region of the medial amygdala, and the central and intercalated amygdalar nuclei. To verify the possible pallial origin of the ventral medial amygdala, we also analyzed pallial and subpallial marker genes in this region during development and in adult specimens. In addition, we labeled radial glia at perinatal stages to reconstruct the radial domain to which the ventral medial amygdala belongs. The results are consistent with a pallial nature of the ventral medial amygdala, while the posterodorsal medial amygdala is subpallial.

Two lateral mouse brain sagittal sections labeled, respectively, for Lypd1 (A) and Kcnab3 (B). (A) Lypd1 labels positively cortical Layers 2 and 5 (less heavily), but only at limbic mesocortical sites, forming the limbic ring that separates the unlabeled isocortex (IsoCx) from the unlabeled hippocampal and olfactory allocortex (Hi, Sub, ERh; OlfCx). The limbic ring is marked twice as the insula (Ins, MCx) and the postrhinal area (PoRh, MCx). (B) Kcnab3, contrarily, labels selectively various layers of the isocortex (IsoCx) and the hippocampal allocortex (Hi, Sub, ERh) but leaves unlabeled selectively the insula (Ins, MCx) and postrhinal (PoRh, MCx) areas of the limbic mesocortical ring, being thus a negative marker for this sort of cortex.

The hippocampal formation is a highly curved and topographically complex forebrain structure. This complex geometry presents persistent challenges for analyzing subregional, laminar, and connectivity patterns. Here, we present a computational workflow that generates curvilinear-coordinate flatmaps from Common Coordinate Framework (CCF) registered hippocampal and retrohippocampal regions by solving the Laplacian equation to derive geodesic streamlines. This transformation unfolds the hippocampus into a planar slab, bounded by the meningeal and ventricular surfaces, with the depth defined along the radial axis. We apply this transform to image volumes, single neuron reconstructions, and point data, including spatial transcriptomic and rabies tracing datasets, revealing topographic variations in the dorsoventral and radial axes that are obscured in the CCF coordinate space. As proof of principle, we use flatmaps to show connectivity loss in a mouse model of Alzheimer's disease and track postnatal development of microglial distribution in the hippocampus. This work provides an efficient and accessible resource for visualizing hippocampal organization across development and disease, offering new opportunities to interrogate the structure and function of this important brain region.

In this commentary, we discuss the concept of field homology, particularly as applied to the brain in comparative neuromorphology. We emphasize its roots in the topological properties of the Bauplan notion (organization plan) as well as in the still scarcely understood concept of developmental fields, and we criticize their modernly frequent erred substitution by the search of similarity of characters. We defend the logical causal connection of embryonic homology with adult homology, irrespective of the regulatory aspects of ontogeny.

Cell type specification in the embryonic brain and spinal cord is thought to begin within molecularly defined progenitor domains that do not intermix. Our data provide an alternative model that is spatially and temporally dynamic within a basal ganglia anlage, the medial ganglionic eminence (MGE). MGE progenitor cells are progressively displaced ventrally and caudally from a rostral growth zone (the MGE/LGE sulcus). Progenitors that leave the MGE/LGE sulcus early occupy caudoventral MGE regions, while ones that leave later reside in rostrodorsal MGE regions. As they change position, their transcriptional states and cell type output change. Transcriptional analyses showed an upregulation of the Nfi TFs during the period of progenitor movement. Nfia and Nfib double mutants alter the repertoire of cortical interneuron subtypes. Overall, we present a mechanism that synchronizes regional patterning with tissue growth and links spatial and temporal specification in producing diverse neuronal subtypes.

The mammalian mesocortex (MCx) was redefined recently as a complete ring intercalated between the allo- and iso-cortex, attending to the consistent expression of 46 selective gene markers. The MCx exhibits various other characteristics such as low myelin content of its fibers, a property directly related to its function and susceptibility to degenerative disorders. Irrespective of its shared molecular profile, the MCx ring differentiates into different sectors with singular molecular and cytoarchitectonic characteristics, such as the posterior orbitary cortex, the cingulate cortex, and the insula. In the present study, using anterograde connectivity experiments published in an Allen Institute for Brain Science public database ( https://brain-map.org/our-research/connectivity ), we analyzed the internal connectivity of the mesocortical ring. We observed that its different sectors are multiply interconnected, possibly achieving integrative functions. The medial posterior orbitary cortex stands out; it appears to play a higher hierarchical role within the MCx ring by sending and receiving projections from all mesocortical sectors.

The limbic connectome is responsible for emotional evaluation and behavioral response to external and internal stimuli. Anxiety, depression, phobias and posttraumatic stress are mental disorders caused by the dysfunction of this system. We compared the pattern of anterograde projections of the full limbic mesocortical ring and the isocortex onto the glutamatergic/pallial amygdala. We used the amygdalar radial model, confirmed by transcriptomic studies, as well as anterograde connectivity experiments published in the Allen Brain Mouse Connectivity Atlas public database ( https://connectivity.brain-map.org/ ). The radial amygdalar model subdivides the glutamatergic amygdala into radial histogenetic-molecularly defined superdomains, domains and subdomains, each stratified in periventricular, intermediate and superficial nuclei. The mesocortical ring projections center onto the basolateral radial amygdalar subdomain and constitute a fundamental pathway in the limbic connectome, whereas the isocortical amygdalar input centers on the lateral radial unit. The mesocortical projections show a medial to lateral topographical distribution between the medial and lateral subdivisions of the basolateral amygdala. Intra-amygdalar connections suggest that computations in the lateral and anterior amygdalar radial domains add layers of complexity to the functions of the basolateral unit. The medial posterior orbitary cortex, proposed previously as the integrative node of the mesocortical ring, projects onto the medial basolateral amygdalar subunit, pointing to this neural structure as an important hub of the limbic system.

This collective eulogy by colleagues, co-authors and friends is a tribute to the work and life of Rudolf Nieuwenhuys. 'Neurofascination' is an apt label for his scholarly life in the sciences from the start in 1955 until his last days in 2024. In addition, he had a broad interest in Roman and Gothic architecture, the history and politics of the twentieth century, religion and the music of Johann Sebastian Bach. Extensive discussions on one or more of these topics often led to long-lasting friendships, some of which inform the following pages. Rudolf is remembered for his highly didactical and remarkably illustrated presentations and publications, including the three-volume The Central Nervous System of Vertebrates and the four editions of The Human Central Nervous System. His research interests addressed an impressively wide range of topics concerning development and evolutionary neurobiology and a systematic approach to comparative brain structures in vertebrates. His almost endless fascination for neuromorphology included the invertebrates as well. But unfortunately, even his long life was not enough to write the book on the comparative neuroanatomy of invertebrates which he long had in mind. The many years of his career spanned the remarkable histology of the gigantocerebellum of mormyrids to an exploratory synthesis of subdivisions of the human cortex, as originally mapped by the Vogt-Vogt school of cortical architectonics.

The mammalian amygdala is located in the temporal lobe of the telencephalon and plays a key role in limbic processing. Recently, our group proposed a radial morphological model to understand the glutamatergic (pallial) part of this nuclear complex in terms of separate progenitor domains. This model explains the amygdala region as consisting of several adjacent developmental radial progenitor units, disposing their distinct periventricular, intermediate, and superficial strata from the ventricle to the pial surface. It was expected that cell populations belonging to specific progenitor domains would present greater molecular similarity to each other than to neighboring developmental units. In this work, we aim to corroborate the existence of several radial domains in the pallial amygdala at the transcriptomic level. snRNAseq experiments in the amygdala of adult mice of both sexes indicated that at low resolution, the whole pallial amygdala was found to divide into two super-radial domains distinguished by differential expression of Slc17a6 and Slc17a7; the former partly imitates molecularly the subpallial (output) amygdalar regions, whereas the rest of the pallial amygdala is molecularly more akin to the surrounding cortical areas. In addition, our snRNAseq transcriptomic analysis fully supports the postulated amygdalar radial model of four main radial domains.

This review summarizes and illustrates the assumptions, structure, and updates that apply to the prosomeric model of brain development. The anteroposterior structure is summarized in terms of tagmata, proneuromeres, and neuromeres. The primary dorsoventral structure relates to the four longitudinal zones of His: the floor, basal, alar, and roof plates. There exists a secondary microzonation of these primary longitudinal zones, and the alar plate domains of the neuromeres seem to show in some cases an anteroposterior tripartition. Topological consideration of the axial bending of the brain and practical consequences as regards section planes is presented. The midline, a fundamental reference, is described in detail in terms of floor, roof, and acroterminal components and landmarks. Finally, the relationship of axonal tracts and blood vessels to the subdivisions in the model is briefly treated.

Ramón y Cajal repeatedly described a diencephalic tegmental tract in mammals, which he wrongly identified as corresponding to Forel’s lenticular tract, while insisting it was formed by fasciculated infrasubthalamic collaterals of the pyramidal tract. These fibers circulated backwards between the zona incerta and the substantia nigra and were lost in the rubral neighborhood, so that their targets remained unknown. The modern literature does not register these pyramidal collaterals at all. In this report, anterograde axon-tracing experiments with motor cortex EGFP injections available at the Allen Mouse Brain Connectivity database were studied to assess whether Ramón y Cajal’s collateral tract exists in the mouse and, in that case, examine the issue of its missing targets. All Allen motor cortex experiments showed straightforwardly the tract described by Ramón y Cajal, which he had lost at midcourse because it diverges into the mesodiencephalic alar plate. Moreover, it was observed to bifurcate as it enters the diencephalon into a deep medial component not distinguished by Ramón y Cajal, which targets diencephalic and mesencephalic preoculomotor cell populations and the deep ZI and Forel’s field, and a thicker outer component, the part he described, which ascends through intermediate thalamic and pretectal alar structures (PIL, RETh, JcRt, and CoRt) until it ends densely on the paratectal bed nucleus of the brachium of the superior colliculus (BSC). The latter is frequently misinterpreted as a lateral part of the SC. Other midbrain targets included the rubral area, the MRt, a novel bilateral reticular endorubral field (ERF), and the preisthmic cuneiform nucleus (Cnf).

At the end of 2023, the Whole Mouse Brain Atlas was announced, revealing that there are about 5300 molecularly defined neuronal types in the mouse brain. We ask whether brain models exist that contemplate how this is possible. The conventional columnar model, implicitly used by the authors of the Atlas, is incapable of doing so with only 20 brain columns (5 brain vesicles with 4 columns each). We argue that the definition of some 1250 distinct progenitor microzones, each producing at least 4–5 neuronal types over time, may be sufficient. Presently, this is nearly achieved by the prosomeric model amplified by the secondary dorsoventral and anteroposterior microzonation of progenitor areas, plus the clonal variation in cell types produced, on average, by each of them.

This study reevaluates the conventional understanding of midbrain anatomy and neuroanatomical nomenclature in the context of recent genetic and anatomical discoveries. The authors assert that the midbrain should be viewed as an integral part of the forebrain due to shared genetic determinants and evolutionary lineage. The isthmo-mesencephalic boundary is recognized as a significant organizer for both the caudal midbrain and the isthmo-cerebellar area. The article adopts the prosomeric model, redefining the whole brain as neuromeres, offering a more precise depiction of brain development, including processes like proliferation, neurogenesis, cell migration, and differentiation. This shift in understanding challenges traditional definitions of the midbrain based on external brain morphology. The study also delves into the historical context of neuroanatomical models, including the columnar model proposed by Herrick in 1910, which has influenced our understanding of brain structure. Furthermore, the study has clinical implications, affecting neuroanatomy, neurodevelopmental studies, and the diagnosis and treatment of brain disorders. It emphasizes the need to integrate molecular research into human neuroanatomical studies and advocates for updating neuroanatomical terminology to reflect modern genetic and molecular insights. The authors propose two key revisions. First, we suggest reclassifying the isthmo-cerebellar prepontine region as part of the hindbrain, due to its role in cerebellar development and distinct location caudal to the genetically-defined midbrain. Second, we recommend redefining the anterior boundary of the genetically-defined midbrain to align with genetic markers. In conclusion, the authors highlight the importance of harmonizing neuroanatomical nomenclature with current scientific knowledge, promoting a more precise and informed understanding of brain structure, which is crucial for both research and clinical applications related to the human brain.

Brain models present a viewpoint on the fundamental structural components of the brain and their mutual organization, generally relative to a particular concept of the brain axis. A model may be based on adult brain structure or on developmental morphogenetic aspects. Brain models usually have functional implications, depending on which functional properties derive from the postulated organization. This essay examines the present scenario about brain models, emphasizing the contrast between columnar or other longitudinal models and transverse subdivisional neuromeric models. In each case, the main functional implications and apparent problems are explored and commented. Particular attention is given to the modern molecularly based ‘prosomeric model’, which postulates a set of 20 transverse prosomeres as the developmental units that serve to construct all the cerebral parts and the particular typology of many different neuronal populations within the forebrain and the hindbrain, plus a number of additional spinal cord units. These metameric developmental units (serially repeated, but with unique molecular profiles) confer to this model remarkable functional properties based mainly on its multiplicity and modularity. Many important brain functions can be decomposed into subfunctions attended to by combined sets of neuronal elements derived from different neuromeres. Each neuromere may participate in multiple functions. Most aspects related to creation of precise order in neural connections (axonal navigation and synaptogenesis) and function is due to the influence of neuromeric anteroposterior and dorsoventral positional information. Research on neuromeric functionality aspects is increasing significantly in recent times.

Classical studies of the avian diencephalon hardly mention the habenulo-interpeduncular tract (a.k.a. retroflex tract), although both the habenula (HB) (its origin) and the interpeduncular nuclear complex (its target) are present. Retroflex tract fibers were described at early embryonic stages but seem absent in the adult in routine stains. However, this tract is a salient diencephalic landmark in all other vertebrate lineages. It typically emerges out of the caudal HB, courses dorsoventrally across thalamic alar and basal plates just in front of the thalamo-pretectal boundary, and then sharply bends 90 degrees caudalwards at paramedian basal plate levels (this is the "retroflexion"), to approach longitudinally via paramedian pretectum and midbrain the rostralmost hindbrain, specifically the prepontine median interpeduncular complex across isthmus and rhombomere 1. We systematize this habenulo-interpeduncular course into four parts named subhabenular, retrothalamic, tegmental, and interpeduncular. We reexamined the chicken habenulo-interpeduncular fibers at stages HH30 and HH35 (6.5- and 9-day incubation) by mapping them specifically with immunoreaction for BEN protein, a well-known marker. We found that only a small fraction of the stained retroflex tract fibers approaches the basal plate by coursing along the standard dorsoventral pathway in front of the thalamo-pretectal boundary. Many other habenular fibers instead diverge into atypical dispersed courses across the thalamic cell mass (implying alteration of the first subhabenular part of the standard course) before reaching the basal plate; this dispersion explains their invisibility. A significant number of such transthalamic habenular fibers cross orthogonally the zona limitans (ZLI) (the rostral thalamic boundary) and invade the caudal alar prethalamus. Here, they immediately descend dorsoventrally, just rostrally to the ZLI, until reaching the prethalamic basal plate, where they bend (retroflex) caudalwards, entering the thalamic basal paramedian area. These atypical fibers gradually fasciculate with the other groups of habenular efferent fibers in their final longitudinal approach to the hindbrain interpeduncular complex. We conclude that the poor visibility of this tract in birds is due to its dispersion into a diversity of atypical alternative routes, though all components eventually reach the interpeduncular complex. This case merits further analysis of the diverse permissive versus nonpermissive guidance mechanisms called into action, which partially correlate distinctly with successive diencephalic, mesencephalic, and hindbrain neuromeric fields and their boundaries. The retroflex tract is a prominent diencephalic landmark in vertebrates but seems absent in adult avian. Here, using BEN immunohistochemistry that specifically identifies fibers of this tract, we study their distribution from the habenular region to the interpeduncular complex. We found that many habenular fibers diverge in an atypical dispersed course through the thalamic cell mass and toward the prethalamic region (top figure). The diagram shows the atypical course of the fibers. image

Data mining was performed at the databases of the Allen Institute for Brain Science () searching for genes expressed selectively throughout the adult mouse mesocortex (transitional cortex ring predicted within the concentric ring theory of mammalian cortical structure, in contrast with central isocortex [ICx] and peripheral allocortex). We aimed to explore a shared molecular profile selective of all or most mesocortex areas. This approach checks and corroborates the precision of other previous definitory criteria, such as poor myelination and high kainate receptor level. Another aim was to examine which cortical areas properly belong to mesocortex. A total of 34 positive adult selective marker genes of mesocortex were identified, jointly with 12 negative selective markers, making a total of 46 markers. All of them identify the same set of cortical areas surrounding the molecularly different ICx as well as excluding adjacent allocortex. Four representative mesocortex markers-Crym, Lypd1, Cdh13, and Smoc2-are amply illustrated, jointly with complementary material including myelin basic protein, to check myelination, and Rorb, to check layer 4 presence. The retrosplenial (ReSp) area, long held to be mesocortical, does not share any of the 46 markers of mesocortex and instead expresses Nr4a2 and Tshz2, selective parahippocampal allocortex markers. Moreover, it is not hypomyelinic and lacks a Rorb-positive layer 4, aspects generally present in mesocortex. Exclusion of the ReSp area from the mesocortex ring reveals the latter to be closed at this locus instead by two adjacent areas previously thought to be associative visual ICx (reidentified here molecularly as postsplenial and parasplenial mesocortex areas). The concepts of ICx, mesocortex, and parahippocampal allocortex are thus subtly modified by substantial molecular evidence. Sagittal section of adult mouse brain showing selective layer2 expression of gene Lypd1 at the insular (Ins) and postrhinal (PoRh) cortex, representing rostrolateral and caudal parts of the mesocortical ring, with negative surrounding isocortical and allocortical areas. image