Introduction

Neuroscience knowledge continues to increase every year (Eke et al., 2022; Yeung et al., 2017), making it challenging for researchers to keep abreast of mounting data and evolving information even in their own domain of expertise. Large-scale endeavors, such as the Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative (Insel et al., 2013) and the European Union’s Human Brain Project (Amunts et al., 2016), are contributing to this tremendous growth along with the ‘long tail’ of independent labs and individual scientists (Ferguson et al., 2014). A key organizing principle for neuroscience knowledge is the seminal notion of neuron types (Petilla Interneuron Nomenclature Group et al., 2008; Zeng and Sanes, 2017), which constitute the conceptual ‘parts list’ of functional circuits. The National Institutes of Health launched the BICCN (see abbreviations in Materials and Methods) to help establish a comprehensive reference of the cell type diversity in the human, mouse, and non-human primate brains (BRAIN Initiative Cell Census Network, 2021). This multi-institution collaboration is already producing innovative results (Muñoz-Castañeda et al., 2021) and actionable community resources (BICCN Data Ecosystem Collaboration, 2022).

Hippocampome.org is an open-access knowledge base of the rodent hippocampal circuit (dentate gyrus, CA3, CA2, CA1, subiculum, and entorhinal cortex) at the mesoscopic level of neuron types (Wheeler et al., 2015). This resource has proven popular and effective thanks to the adoption of a simple yet powerful classification system for defining neuron types. Specifically, a key property for the identification of neuron types in Hippocampome.org is the location of axons and dendrites across the subregions and layers of the hippocampal formation. This approach can be broadly extended to classify neurons in other brain regions and neural systems (Ascoli and Wheeler, 2016). Focusing on axonal and dendritic distributions provides two considerable advantages. First, these features mediate neuronal connectivity, thus immediately revealing the underlying blueprint of network circuitry (Rees et al., 2017). Second, they are widely used in the neuroscience community as a reliable and concrete anchoring signature to correlate electrophysiological and transcriptomic profiles (DeFelipe et al., 2013). Therefore, starting from the foundational morphology-based identification of 122 neuron types in the first release (version 1.0 or v1.0), Hippocampome.org progressively amassed an increasing amount of complementary data, such as firing patterns, molecular expression, cell counts, synaptic communication, in vivo oscillations, and connection probabilities. In all cases, the public repository provided direct links to the specific peer-reviewed empirical evidence supporting the added knowledge.

Having established a web-based integrated storehouse of hippocampal information, Hippocampome.org also expanded its scope by including data-driven computational models of neuronal excitability and synaptic signaling, as well as ties to community resources such as NeuroMorpho.Org (Akram et al., 2018), SenseLab ModelDB (McDougal et al., 2017), CARLsim (Niedermeier et al., 2022), and the Allen Brain Atlas (Jones et al., 2009). Altogether, these extensions resulted in the emergence of a complete framework for launching real-scale, biologically detailed computer simulations of the hippocampal formation. The present report thus marks a new phase in the life cycle of this community resource. Hippocampome.org v2.0, introduced here, also incorporates over 50 newly identified neuron types, updating the classification to the most recent literature findings.

The following “Description of resource” section begins with a concise, referenced overview of the neural properties collated from Hippocampome.org v1.0 through release v1.12. We then briefly describe the new neuron types and data currently being added in Hippocampome.org v2.0. Next is an abridged summary of the usage and recognition of this online portal in biomedical research. This is followed by an explanation of the latest capabilities to search, filter, and download the complete set of computational parameters enabling quantitative connectomic analyses and spiking neural network simulations. The section concludes with an outlook of possible research applications allowed by the expansion of this scientific resource.

Description of resource

Characterizing properties of hippocampal neuron types

Hippocampome.org v1.0 (Wheeler et al., 2015) established the morphological encoding of axonal and dendritic locations and the main neurotransmitter (glutamate or GABA) as the primary determinants of neuron types in the rodent hippocampal formation. For example, a DG Basket cell (with name capitalized to indicate a formally defined neuron type) is a GABAergic cell with axon contained in the granular layer and dendrites spanning all DG layers (Figures 1A1-4). In this framework, two neurons releasing the same neurotransmitter belong to different types if the axon or dendrites of only one of them invades any of the 26 layers across 6 subregions of the hippocampal formation (hippocampome.org/morphology). In other words, neurons of the same type share the same potential inputs, outputs, and excitatory vs. inhibitory function. These properties were initially supplemented with additional empirical evidence for molecular expression of major protein biomarkers (Figure 1A5; hippocampome.org/markers) and membrane biophysics (Figure 1A6-7; hippocampome.org/electrophysiology).

Figure 1.

Many neuronal properties and functionalities were progressively added in 12 subsequent releases (Table 1). The numerical sequencing of these Hippocampome.org versions depended on the order of peer-review and publication of the corresponding scientific reports. Here we will describe them instead in logical groupings. The first two updates enhanced the user functionality of the knowledge base. Specifically, v1.1 integrated a web-based interactive thesaurus mapping of synonyms and definitions (Hamilton et al., 2017a; hippocampome.org/find-term) to help disambiguate the many terminological inconsistencies in the neuroscience literature (Shepherd et al., 2019; Yuste et al., 2020). Release v1.2 introduced the capability to browse, search, and analyze the potential connectivity between neuron types (Rees et al., 2016; Hippocampome.org/connectivity) as derived from the compiled overlapping locations of all the presynaptic axons and postsynaptic dendrites. Transcriptomic information was greatly expanded in both v1.3 (Hamilton et al., 2017b), which incorporated in situ hybridization data from the Allen Brain Atlas (Lein et al., 2007), and v1.5 (White et al., 2020), which leveraged relational inferences interlinking the region-specific expression of two or more genes.

Table 1.

The quantifications of firing pattern phenotypes, such as rapid adapting spiking, transient stuttering, and persistent slow-wave bursting, in v1.6 (Komendantov et al., 2019; hippocampome.org/firing_patterns) were fitted by dynamical systems modeling (Izhikevich, 2003) in v1.7 (Venkadesh et al., 2019; hippocampome.org/Izhikevich). Although the above properties were largely measured from slice preparations, v1.9 made available measurements from in vivo recordings (Sanchez-Aguilera et al., 2021; hippocampome.org/in-vivo). Release v1.10 provided a compendium of cognitive functions linked to specific hippocampal neurons (Sutton and Ascoli, 2021; hippocampome.org/cognome), while the v1.11 neuron type census estimated the population counts for each neuron type (Attili et al., 2022; hippocampome.org/census). Last but not least are a set of properties pertaining not to individual neuron types but to synaptic connections between a pair of pre- and post-synaptic neuron types. In particular, v1.8 calculated the synaptic probabilities and the numbers of contacts per connected pair (Tecuatl et al., 2021b; hippocampome.org/syn_probabilities), and v1.4 data mined synaptic physiology (Moradi and Ascoli, 2020; hippocampome.org/synaptome), with conductance, time constant, and short-term plasticity values normalized by age, temperature, species, sex, and recording method in v1.12 (Moradi et al., 2022; hippocampome.org/synapse), leveraging machine learning and a phenomenological model (Tsodyks et al., 1998).

Expanding the catalog of neuron types and properties from Hippocampome.org v1.x to v2.0

The Hippocampome.org framework to classify neuron types and collate their properties allows agile content updates as new data are continuously reported in the peer-reviewed literature. For example, the description of a parvalbumin-positive DG GABAergic interneuron with axon contained in the granular layer and dendrites invading the molecular layer but not the hilus (Vaden et al., 2020) supported the definition of a new neuron type (Figures 1B1-5), referred to in Hippocampome.org v2.0 as DG Basket GRALDEN. Moreover, such an identification made it possible to unequivocally ascribe to this neuron type previously reported electrophysiological characteristics (Figures 1B6-7; Markwardt et al., 2011). Comprehensive literature mining following the same process expanded the Hippocampome.org v2.0 catalog with 51 new neuron types¹ across 5 of the 6 subregions of the hippocampal formation (Figure 2), including axonal-dendritic morphological patterns (Figure 2A), molecular expression (Figure 2B), and membrane biophysics (Figure 2C).

Figure 2.

Besides identifying new neuron types, the Hippocampome.org classification system also allows the ongoing accumulation of new properties onto existing neuron types as well as the reconciliation of fragmented descriptions from scientific publications (Figure 3). For instance, converging evidence indicates that EC Layer III Pyramidal cells have axonal projections in all layers of CA1 (Deller et al., 1996; Takács et al., 2012), not just in stratum lacunosum-moleculare (SLM) as originally reported (Steward, 1976). Hippocampome.org v2.0 captures both the new extracted knowledge and the corresponding experimental evidence (Figure 3A). The annotation of neuron type-specific firing phases relative to in vivo oscillations in v1.9 highlighted a clear distinction between Superficial and Deep CA1 Pyramidal cells (Sanchez-Aguilera et al., 2021). The present release enriches that description with accompanying novel molecular markers (Figure 3B1), membrane biophysics values (Figure 3B2), and differential connectivity with other subregions and neuron types (Figure 3B3). Similarly, numerous additional firing patterns (Figure 3C) have been datamined for existing neuron types, such as adapting spiking in CA3 Basket cells and non-adapting spiking in CA3 Bistratified cells (Fidzinski et al., 2015) or transient stuttering in CA1 Radiatum Giant cells (Kirson and Yaari, 2000). Notably, this includes a novel phenotype, TSTUT.PSTUT in CA1 Interneuron Specific O-targeting QuadD cells (Chamberland et al., 2010). With this report, we also release new differential connection probabilities to various CA1 neuron type targets from traditional CA3 Pyramidal cells vs. CA3c Pyramidal cells (Figure 3D) and from DG Granule cells to mossy fiber CA3 targets (Table 2).

Figure 3.

Table 2.

Quantifying the content and impact of Hippocampome.org

Over the course of subsequent releases, we have measured Hippocampome.org content using two metrics. The number of pieces of knowledge (PoK) tallies the distinct units of structured information, such as the statements that DG Granule cell axons invade the hilus or that CA1 Basket cells express parvalbumin. The pieces of evidence (PoE) are specific excerpts of peer reviewed publications (portion of text, figure, or table) or database entries (e.g., from the Allen Brain Atlas) always linked to each PoK. Both PoK and PoE continued to grow with successive releases of Hippocampome.org (Figure 4A). Notably, the largest increases in PoK and PoE were related to synaptic properties (Moradi and Ascoli, 2020; Tecuatl et al., 2021b; Moradi et al., 2022). Specifically, the data underlying synaptic physiology and connection probabilities were supported by over 23,000 PoE and yielded a remarkable 500,000 PoK thanks to the normalized collection of signaling and short-term plasticity modeling parameters for multiple combinations of experimental conditions.

Figure 4.

To assess community usage of Hippocampome.org, we tracked the number of citations of the original publication (Wheeler et al., 2015) and of the subsequent versions (Figure 4B), separating simple references from actual employment of information extracted from Hippocampome.org for secondary analyses (Table 3). At the time of this writing, year 2021 proved to be the most prolific citation-wise; however, more than a third of the releases (v1.8-12) appeared after 2021 and most PoK were added in 2022, so usage could potentially accelerate further in coming years. An early application of Hippocampome.org-sourced data used subthreshold biophysical measures, such as input resistance and membrane time constant, for multicompartmental models of signal integration and extracellular field generation (Gulyas et al., 2016). That study concluded that somatic and proximal dendritic intracellular recordings in pyramidal cells and calretinin-positive interneurons, in particular, do not capture a sizable portion of the synaptic inputs. As a recent usage example, another lab employed Hippocampome.org as the primary information resource for neuron types in DG, CA3, and CA1 (Schumm et al., 2022). They discovered that mild traumatic brain injury, in the form of alterations in spike-timing-dependent plasticity, may affect the broadband power in CA3 and CA1 and the phase coherence between CA3 and CA1.

Table 3.

From experimental data to biologically realistic computational models

Several key neural properties collated into Hippocampome.org have gradually transformed the site from an organized repository of hippocampal knowledge to a computational framework for launching real-scale neural network simulations. Specifically, building a data-driven circuit model of a neural system (such as the hippocampal formation or portion thereof) requires four essential quantities besides the full list of neuron types (Bahmer et al., 2023; DePasquale et al., 2023): (i) the number of neurons in each type; (ii) the input-output response function for each neuron type; (iii) the connection probability for each pair of interacting neuron types; and (iv) the unitary synaptic signals for each pair of connected neuron types (Figure 5). Of those quantities, (i) and (ii) are neuron type properties, while (iii) and (iv) are properties of directional connections, defined as a distinct pair of a presynaptic and a postsynaptic neuron type. Moreover, (i) and (iii) are structural features, while (ii) and (iv) are electrophysiological ones.

Figure 5.

Hippocampome.org v2.0 provides estimates of the number of neurons in each neuron type (i) for both rats and mice (Figure 5A). These values were derived in a two-step process (Attili et al., 2020): first, literature mining extracted suitable quantitative relations such as the cellular density in a given layer (Attili et al., 2019), the total count of neurons expressing a certain gene, or the fraction of sampled cells with a particular morphology; second, numerical optimization of the corresponding equations yielded a complete census for all neuron types. Hippocampome.org represents the neuronal input-output response function (ii) in the form of single- and multi-compartment Izhikevich models (Figure 5B) fitted by evolutionary algorithms to accurately reproduce the observed firing behavior of each neuron type (Venkadesh et al., 2018). The connection probability (iii) from one neuron type to another (Figure 5C) was computed from measurements of the appropriate axonal and dendritic lengths in each invaded subregion and layer (hippocampome.org/A-D_lengths). Additionally, users can also access the presynaptic and postsynaptic path distances from the respective somata (hippocampome.org/soma_distances) and the number of contacts per connected neuron pairs (hippocampome.org/num_contacts). As for the synaptic communication between neurons (iv), Hippocampome.org adopts the Tsodyks-Pawelzik-Markram formulation, representing unitary signals and short-term plasticity with five constants for each directional pair of interacting neuron types: the synaptic conductance, decay time, recovery time, facilitation time, and the utilization ratio (Tsodyks et al., 1998; Moradi et al., 2022). Once again, these parameters were fitted from the experimental data (Moradi and Ascoli, 2018) employing deep learning to account for (and predict the effects of) numerous experimental variables (Figure 5D), including species (rat vs. mouse), sex (male vs. female), age (young vs. adult), recording temperature (room vs. body), and clamping configuration (voltage vs. current).

The above description underscores the crucial interconnectedness of individually measured neuronal properties forming a cohesive whole in Hippocampome.org (Figure 6). In particular, normalized simulation parameters (e.g., the sensitivity of recovery variable in Izhikevich models) are derived from quantitative experimental measurements, such as the spiking adaptation rate (Figure 6a). Those in turn are linked to an identified neuron type based on qualitative features, like calbindin expression or laminar distribution of axons and dendrites. In addition to enabling computational applications as described below, such integration also allows the meta-analysis of correlations between morphological features, molecular profiles, electrophysiological properties, and dynamic circuit functions. At the same time, several components of Hippocampome.org are also synergistically linked to external community resources (Figure 6B). For example, each neuron page links out to all three-dimensional morphological reconstructions of the same cell type available in NeuroMorpho.Org (Ascoli et al., 2007), and selected data from NeuroMorpho.Org were used to compute axonal and dendritic length and connection probabilities. Each neuron page also links out to all computational models (including Hodgkin-Huxley, stochastic diffusion, mean firing rate, etc.) involving the same cell type on ModelDB (McDougal et al., 2017), while conversely ModelDB includes the Izhikevich models for all Hippocampome.org neuron types. Moreover, simulation parameters from Hippocampome.org are exportable to the CARLsim simulation environment (Nageswaran et al., 2009), enabling fast execution of spiking neural network models optimized for GPUs. Furthermore, Hippocampome.org harnessed data from the Allen Brain Atlas (Lein et al., 2007) to infer gene expression for principal neurons and cell densities for use in the neuron type census.

Figure 6.

To facilitate construction of spiking neural network simulations, Hippocampome.org v2.0 also includes a new graphical user interface (GUI)². With this GUI, users can download sets of simulation parameter values for arbitrarily selected neuron types, a subregion of interest, or the whole hippocampal formation (Figure 7). The sets consist of files for the instantiation of CARLsim simulations and a CSV spreadsheet of parameters for use in a different simulation environment of the user’s choice. For the convenience of users interested in simplified circuit models, Hippocampome.org informally ranks the importance of each neuron type from 1 (essential) to 5 (dispensable). For instance, a user may choose to simulate only the canonical, or rank 1, neuron types of the tri-synaptic circuit and entorhinal cortex, consisting of DG granule, CA3 pyramidal, CA1 Pyramidal, and MEC LII Stellate cells. When Hippocampome.org is missing a parameter value due to insufficient experimental evidence, the GUI exports a default value clearly indicating so in the downloadable files. For missing Izhikevich and synaptic signaling parameters, the default values are those provided by the CARLsim simulation environment. For missing synaptic probabilities, Hippocampome.org precomputes values averaged by connection type, namely excitatory-excitatory (0.0117), excitatory-inhibitory (0.0237), inhibitory-excitatory (0.00684), and inhibitory-inhibitory (0.00423).

Figure 7.

Potential applications to connectomic analyses and spiking neural networks simulations

Hippocampome.org v2.0 enables the multiscale analysis of circuit connectivity (Figure 8). At the highest echelon are the connections between hippocampal subregions, which are comprised of the mesoscopic level potential connectivity between individual neuron types (Figure 8A). Expanding, for example, upon the 147 connections between DG and CA3 neuron types reveals all the connections every individual neuron type forms with the other neuron types within and across the subregions (Figure 8B). Zooming in onto a single neuron type each from DG and CA3, it is possible to quantify the efferent and afferent connections with other neuron types from throughout the hippocampal formation in terms of synaptic probabilities and number of neuronal partners (Figure 8C). Diving even deeper into the isolated connection between two neuron types, such as the mossy fiber contacts from DG Granule cells to CA3 Basket cells, expands the connectivity analysis to several physiological factors affecting neuronal communication: the subcellular location of the synaptic contact (e.g., soma in stratum pyramidale and proximal dendrites in stratum lucidum), the transfer function (product of synaptic conductance and decay time constant), the in vivo firing rate of the presynaptic neuron type, and the relationship between input current and resulting output spiking frequency (F-I curve) of the post-synaptic neuron (Figure 8D).

Figure 8.

Release of v2.0 makes the original objective of Hippocampome.org, to enable data-driven spiking neural network simulations of rodent hippocampal circuits (Ascoli, 2010), finally achievable. An ongoing line of research in this regard focuses on a real-scale mouse model of CA3, with the eventual goal of investigating the cellular mechanisms of pattern completion. Initial work included excitatory Pyramidal cells and seven main inhibitory interneuron types: Axo-axonic, Basket, Basket CCK+, Bistratified, Ivy, Mossy Fiber-Associated ORDEN, and QuadD-LM (Kopsick et al., 2022). Use of Hippocampome.org parameters for cell census, Izhikevich models, synaptic signals, and connection probabilities resulted in robust, realistic, rhythmic resting state activity for all neuron types (Figure 9A). Another pursuit seeks to replicate the spatial representation in grid cells (Sargolini et al., 2006), modeled utilizing the Hippocampome.org MEC LII Stellate cells and supported by various GABAergic interneuron types (Dhillon and Jones, 2000). This study aims to reproduce the in vivo firing of these neuron types as a virtual rodent explores an open field (Figure 9B). While preliminary, these illustrative examples highlight the potential of Hippocampome.org-enabled data-driven spiking neural network simulations to investigate computational theories of cognitive functions in hippocampal circuits at the level of biologically detailed mechanisms (Sutton and Ascoli, 2021).

Figure 9.

Discussion

Hippocampome.org, through its continuous updates and conspicuous usage, has established itself prominently amongst other readily accessible, evidence-based, expert-curated bioscience public resources of note, such as FlyBase for Drosophila molecular biology (The FlyBase Consortium, 1994; dos Santos et al., 2015), WormBase for nematode genomics (Stein et al., 2001), the Blue Brain Project for somatosensory cortex (Markram, 2006), SynGO for synaptic functions (Koopmans et al., 2019), and RegenBase for spinal cord injury biology (Callahan et al., 2016).

The growth of Hippocampome.org since the initial release of v1.0 (Wheeler et al., 2015) has been prodigious. To date, the site has been visited over 136,000 times with over 33,000 unique visits, and the original publication has been cited more than hundred times. Each successive release of Hippocampome.org has added new dimensions of knowledge and/or functionality and has been building toward assembling all the components necessary to produce real-scale computational models of the rodent hippocampal formation. The culmination of all this work is the release of v2.0, which introduces a framework for launching computer simulations directly from the accumulated knowledge. However, achieving simulations does not mark the end point for this project, because Hippocampome.org will continue to aggregate new knowledge as it is published in the peer-reviewed literature. Gradually, the focus of this resource will shift from development to exploitation through the in silico emulation of complex dynamics observed in vivo and in vitro, with the goal of shedding light on the underlying synaptic-level computational mechanisms.

The creation of real-scale spiking neural network models of the hippocampal formation and its subregions can foster biologically realistic, data-driven, mesoscopic simulations of cognitive function and dysfunction (Sutton and Ascoli, 2021). For instance, simulations with Hippocampome.org’s real-scale model of the dentate gyrus can build on previous network models of epileptogenesis (Dyhrfjeld-Johnsen et al., 2007) by providing further clarity to the roles of all documented neuron types and their corresponding potential connections in seizure initiation and propagation. A real-scale model of CA1 can aim to further the insights into the spatiotemporal dynamics of the circuit during theta oscillations (Bezaire et al., 2016; Navas-Olive et al., 2020; Romani et al., 2023). Furthermore, network models involving multiple subregions can open new vistas on unexplored territories, such as the use of real-scale models of the entorhinal cortex and CA2 to simulate the neuron- and connection-type specific mechanisms of social memory (Lopez-Rojas et al., 2022). Moreover, open source sharing of the real-scale models replicating those functions (Gleeson et al., 2017) will facilitate cross-talk within the systems neuroscience community to better understand the role of distinct neuron types in hippocampal function.

A notable aspect of Hippocampome.org is that all freely downloadable model parameters are directly linked to the specific peer-reviewed empirical evidence from which they were derived. Thus, if users disagree with a specific interpretation, or are not fully convinced by an individual experimental measurement, they maintain control in selecting the information sources. Conversely, researchers can choose to reuse the collated experimental data to constrain different computational models they may prefer, such as adopting the Hodgkin-Huxley formalism instead of Izhikevich dynamics. At the same time, Hippocampome.org is not only a collection of model parameters and corresponding empirical evidence, but it also provides an opportunity to unearth knowledge gaps, as facilitated by an intuitive search functionality (hippocampome.org/find-neuron). Missing data can serve to guide the design of targeted “low hanging fruit” experiments or to generate new hypotheses.

Another important element of Hippocampome.org is the careful annotation of the experimental metadata for each piece of evidence, including the species (rat or mouse), sex (male or female), age (young or adult) as well as any and all reported details that could affect the recorded neuronal property. Examples of these confounding factors abound especially for in vitro electrophysiological data, such as the exact chemical composition of the solution in the electrode and in the bath, slice thickness and orientation, clamping configuration, recording temperature, and animal weight. Because these covariates, when reported by the original investigators, are also stored in the database, it is possible to account for them in subsequent analyses and simulations. Hippocampome.org therefore constitutes a considerably rich one-stop resource to compare and “translate” key parameters, such as the amplitude and duration of a synaptic signal between two specifically identified neuron types, for instance, from 14 day old male rat at 22 °C in voltage clamp to a 56 day old female mouse at 32 °C in current clamp. When fed into spiking neural network simulations, these differential parameter values can foster intuition while attempting to reconcile neuroscience theories and observations.

Hippocampome.org is yet poised for the onset of an information deluge from current and future big science projects, which will need to be integrated into a complete cohesive picture (de La Prida and Ascoli, 2021). Although morphological identification will continue to play a fundamental role in defining neuron types and circuit connectivity, the manner in which knowledge is cross-referenced in this resource will allow its effective linkage to rapidly accumulating molecular and imaging data. The ongoing spatial transcriptomics revolution is already transforming the frontiers of cellular neuroscience, often using the hippocampus as its favorite sandbox (Lein et al., 2017; Yao et al., 2021; Zeisel et al., 2015). Single-cell transcriptomics via scRNAseq can bolster the current morphological information by offering distinct transcription factor codes for existing neuron types and assist in defining new ones (Cembrowski and Spruston, 2019; Winnubst et al., 2020; Yuste et al., 2020). From the functional side, optical imaging via genetically encoded voltage indicators (Knöpfel and Song, 2019) will provide in vivo voltage traces for defined neuron types that can greatly enhance the repertoire of firing pattern phenotypes to utilize in simulations (Adam et al., 2019). Data-driven computational models can provide a useful conceptual bridge between molecular sequencing and activity imaging by investigating the effects of specific subcellular distributions of voltage- and ligand-gated conductances on neuronal excitability (Migliore et al., 2018). With the converging maturation of these young techniques and the advent of others yet on the horizon, Hippocampome.org will be able to integrate multidimensional knowledge on the solid foundation of neuronal classification.

Materials and Methods

Hippocampome.org v2.0 vs. the legacy status of v1.12

With the release of v2.0 of Hippocampome.org upon publication of this article, v1.12 of the website will no longer be updated and will transition to legacy status (hippocampome.org/legacy_v1). In this way, users may avail themselves of the full benefits of the new content and functionality of v2.0, while maintaining access to reference content as published through v1.12. In the near term, neuron types new to v2.0 are tagged with an asterisk on the web site to differentiate them from v1.1x types.

Linking neuron types to NeuroMorpho.Org morphological reconstructions

Hippocampome.org neuron types are regularly linked to appropriately identified digital reconstructions of neuronal morphology from NeuroMorpho.Org (Ascoli et al., 2007). Identification of suitable reconstructions with individual neuron types depends on the correspondence of dendritic and axonal locations across hippocampal subregions and layers, as they appear in the reference publication. Alternatively, direct cell typing by the authors in the reference publication text is accepted as evidence for canonical (principal cell) types, such as CA1 pyramidal cells or DG granule cells. Reconstructions are not linked to a neuron type if the experimental conditions are inconsistent with the inclusion criteria of Hippocampome.org, as in the case of cell cultures or embryonic development. Lack of either axonal or dendritic tracing also disqualifies reconstructions of non-canonical neurons from being linked.

Connections from DG Granule cells to CA3

To compute estimates of connection probabilities and numbers of contacts per connected pair for the rat mossy fiber-CA3 circuit, we used previously calculated average convex hull volume (Tecuatl et al., 2021b) and several measurements from a seminal anatomical study (Acsády et al., 1998): DG Granule cell axonal length within CA3 (3,236 µm), inter-bouton distances for mossy boutons on Pyramidal cell targets in CA3c (162 µm) and in the rest of CA3 (284 µm), and inter-bouton distances for en-passant and filipodia boutons onto CA3 interneurons (67.4 µm, considering that 48 interneurons can be contacted by a single GC). Given that the mossy fibers innervate mainly CA3 SL, and due to the lack of information regarding the exact proportion of axons innervating CA3 SP, these calculations assume that GCs only innervate SL. The probabilities of connection and numbers of contacts per connected pair (Table 2) are estimated as previously described (Tecuatl et al., 2021a) utilizing the CA3 dendritic lengths reported in Hippocampome.org.

Connections from CA3 and CA3c Pyramidal cells to CA1

To compute estimates of connection probabilities and numbers of contacts per connected pair for the rat Schaffer collaterals-CA1 circuit, we utilized previously reported values for the distinct axonal innervation patterns (Ropireddy et al., 2011; Sik et al., 1993; Wittner et al., 2007) in CA1 SR and SO from CA3 Pyramidal cells (27.5% of total axonal length: 64% to SR, 15% to SP, 21% to SO) and CA3c Pyramidal cells (64.1% of total axonal length: 94% to SR, 3% to SP, 3% to SO). In addition, we used the average inter-bouton distance reported for the Schaffer collaterals (Li et al., 1994) in SR (4.47 µm) and SO (5.8 µm). Total axonal length was measured with L-Measure (Scorcioni et al., 2008) from three NeuroMorpho.Org reconstructions for CA3c (NMO_00187, NMO_00191) and CA3b (NMO_00931). We extracted parcel-specific convex hull volumes from Janelia MouseLight (Winnubst et al., 2019) Pyramidal cell reconstructions (AA0304, AA0307, AA0420, AA0960, AA0997, AA0999, AA1548) mapped to the 2022 version of the Allen Institute Common Coordinate Framework (CCF). The probabilities of connection and number of contacts per connected pair were estimated as previously described (Tecuatl et al., 2021a) using CA1 dendritic lengths from Hippocampome.org. We used separate values for inter-bouton distances in CA1 SR for CA3c Pyramidal cells (5.5 µm: Wittner et al., 2007) and CA3 Pyramidal cells (3.7 µm: Shepherd et al., 2002; 4.4 µm: Li et al., 1994; 4.29 µm: Sik et al., 1993; averaged as 4.1 µm).

Constructing Hippocampome.org spiking neural simulations

Hippocampome.org utilizes CARLsim (Nageswaran et al., 2009) as its default simulation environment (socsci.uci.edu/∼jkrichma/CARLsim/). CARLsim is a graphics processing unit (GPU)-accelerated library of functions for simulating spiking neural networks based on Izhikevich neuron models (Izhikevich, 2003). The current version is CARLsim 6 (Niedermeier et al., 2022), and the most up-to-date Hippocampome.org-optimized code base, including features not yet released in the main CARLsim version, can be found at hippocampome.org/CARLsim (Kopsick et al., 2022).

Web portal, database, and source code

Hippocampome.org runs on current versions of Chrome, Safari, and Edge web browsers, and it is deployed on a CentOS server running Apache. The website runs off of PHP from a MySQL database. The code for Hippocampome.org is available open source at github.com/Hippocampome-Org. This includes all code for displaying the pages of the website, all scripts for importing spreadsheets into the database, code for using evolutionary algorithms to optimize Izhikevich model parameters, code for the graph theory analysis of the potential connectome, code for the implementation of the firing pattern classification algorithm, and code for analyzing network simulations in CARLsim.

Glossary of abbreviations

• 5HT-3: serotonin receptor 3

• AA: EC LII Axo-axonic cell

• AAC: Axo-axonic cell

• ABA: Allen Brain Atlas

• AP_ampl: action potential amplitude

• AP_width: action potential width

• ASP.: adapting spiking

• Astn2: astrotactin 2

• BC: Basket cell

• BC MP: EC LII Basket-Multipolar cell

• BiC: Bistratified cell

• BICCN: BRAIN Initiative Cell Census Network

• C: Capacitance

• CB: calbindin

• CB1: cannabinoid receptor type 1

• CCK+: cholecystokinin-positive

• CR: calretinin

• CSV: comma-separated value

• Dcn: decorin

• DG: dentate gyrus

• E-E: excitatory to excitatory

• E-I: excitatory to inhibitory

• EC: entorhinal cortex

• ENK: enkephalin

• fAHP: fast after-hyperpolarizing potential

• g: conductance constant

• GABAa α1: GABA-a alpha 1 subunit

• GC: granule cell

• Gpc3: glypican 3

• GPUs: graphical processing units

• GRALDEN: GRAnule-Like DENdrites Garci grid cell

• Grp: gastrin releasing peptide

• GUI: graphical user interface

• H: hilus

• HIPROM: Hilar Interneuron with PRojections to the Outer Molecular layer

• Htr2c: 5-hydroxytryptamine receptor 2c

• I-E: inhibitory to excitatory

• I-I: inhibitory to inhibitory

• IS: interneuron specific

• LI-II: layers 1-2

• LII: layer 2

• LIII: layer 3

• Max FR: maximum firing rate

• MEC: medial entorhinal cortex

• MFA: Mossy Fiber-Associated

• mGluR1a: metabotropic glutamate receptor 1 alpha

• MOCAP: cell with MOlecular Commissural-Associational Pathway-related axons and dendrites

• MOLAX: MOlecular Layer Axons

• MP PC: EC LI-II Multipolar Pyramidal cell

• Mus2R: muscarinic type 2 receptor

• NASP: non-adapting spiking

• Ndst4: N-deacetylase and N-sulfotransferase 4

• nNOS: neuronal nitric oxide synthase

• Nov: nephroblastoma overexpressed

• NPY: neuropeptide Y

• Nr3c2: nuclear receptor subfamily 3 group C member 2

• Nr4a1: nuclear receptor subfamily 4 group A member 1

• ORAX: ORiens AXons

• ORDEN: ORiens DENdrites

• PC: pyramidal cell / CA1 Pyramidal cell (Fig. 9B)

• PL: polymorphic layer

• PoE: pieces of evidence

• PoK: pieces of knowledge

• Prss12: serine protease 12

• Prss23: serine protease 23

• PV+: parvalbumin-positive

• QuadD-LM: quadrilaminar dendrites – lacunosum-moleculare

• R_in: input resistance

• RLN: reelin

• sAHP: slow after-hyperpolarizing potential

• SC: MEC LII Stellate cell

• SD: standard deviation

• SG: stratum granulosum

• SL: stratum lucidum

• SLM: stratum lacunosum-moleculare

• SMi: inner stratum moleculare

• SMo: outer stratum moleculare

• SO: stratum oriens

• SOM: somatostatin

• SP: stratum pyramidale

• SR: stratum radiatum

• Sub: subiculum

• SWR: sharp-wave ripple

• SynGO: synaptic gene ontologies

• T: Temperature

• τ_d: synaptic decay constant

• τ_f: facilitation time constant

• τ_m: membrane time constant

• τ_r: recovery time constant

• TPM: Tsodyks-Pawelzik-Markram

• TSTUT.: transient stuttering

• TSTUT.PSTUT: transient stuttering followed by persistent stuttering

• TSTUT.SLN: silence preceded by transient stuttering

• U: utilization ratio

• vGluT3: vesicular glutamate transporter 3

• V_h: holding potential

• VIP: vasoactive intestinal polypeptide

• V_min: post-spike reset potential

• V_peak: spike cutoff potential

• V_r / V_rest: resting membrane potential

• V_t / V_thresh: firing threshold potential

• WA BC: Wide-arbor Basket cell

• Wfs1: wolframin ER transmembrane glycoprotein

Acknowledgements

We thank David J. Hamilton, Charise M. White, Christopher L. Rees, Maurizio Bergamino, Keivan Moradi, Siva Venkadesh, Alberto Sanchez-Aguilera, Teresa Jurado-Parras, Manuel Valero, Miriam S. Nokia, Elena Cid, Ivan Fernandez-Lamo, Daniel García-Rincón, Liset M. de la Prida, Sarojini M. Attili, Iqbal Addou, and the many student interns (hippocampome.org/thx) for invaluable help advancing from v1.0 to v2.0.

Competing Interests

The authors have no competing interests.

Contributions

DWW contributed to the conceptualization, methodology, software, investigation, data curation, writing – original draft, visualization, supervision, and project administration. JDK contributed to the methodology, software, formal analysis, investigation, data curation, writing – review and editing, and visualization. NS contributed to the methodology, software, investigation, data curation, writing – review and editing, and visualization. CT contributed to the methodology, validation, formal analysis, investigation, data curation, writing – review and editing, visualization, and supervision. AOK contributed to the formal analysis, writing – review and editing, and visualization. KN contributed to the software and writing – review and editing. GAA contributed to the conceptualization, methodology, resources, investigation, data curation, writing – review and editing, visualization, supervision, project administration, and funding acquisition.

Funding information

This work was supported in part by grants R01NS39600, RF1MH128693, and U01MH114829 from the National Institutes of Health (NIH), and DE-SC0022998 from the Department of Energy (DOE). The funding sources were not involved in study design, data collection and interpretation, or the decision to submit the work for publication.