Hippocampome.org 2.0 is a knowledge base enabling data-driven spiking neural network simulations of rodent hippocampal circuits
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason University, United States
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity, College of Engineering and Computing, George Mason University, United States
- Interdisciplinary Program in Neuroscience, College of Science, George Mason University, United States
Figures
Figure 1
Defining neuron types in Hippocampome.org.
(A) Properties of a Hippocampome.org v1.0 neuron type. (A1) Morphology of a Dentate Gyrus (i) 2232 Basket cell (NeuroMorpho.Org cell NMO_34300: Figure S3A in Hosp et al., 2014) with axons (red) in st…
Figure 2
New neuron types added to Hippocampome.org v2.0.
(A) Morphology encodings of the 56 new neuron types that extend the 124 types in Hippocampome.org v1.12. (Left) Increase in number of neuron types for each subregion. For the neuron type names, …
Figure 3
Extensions to the neuronal properties of Hippocampome.org v1.x.
(A) Additions to the axonal projections (circled in green) for two v1.0 neuron types, based on information derived from Figure 2b in Deller et al., 1996. (B1) Biomarker expressions for the two CA1 …
Figure 4
Trends in Hippocampome.org data, knowledge, citations, and usage since v1.0.
(A) Increase in pieces of knowledge (blue) and evidence (red) with Hippocampome.org version number. (B) Number of citations, in which the publication is simply referenced (blue and gray portions), …
Figure 5
Transitional knowledge enabling Hippocampome.org to support spiking neural network simulations.
Center: General diagram of the hippocampal formation and the number of cell types in Hippocampome.org v1.0. (A) Neuron type census. Top: General pipeline for obtaining cell counts for specific …
Figure 6
Hippocampome.org data provenance.
(A) The internal web of constituent neuron-type properties (black thin arrows) that ultimately contribute to the instantiation of spiking neural simulations (orange thick arrows). Properties …
Figure 7
CARLsim simulation parameters selection and file generation interface.
(A) The user chooses which subset of the available neuron types to include in the generated downloadable parameter file. Neuron types can be selected (check boxes and gray highlights) either …
Figure 8
Hierarchy of neuronal connectivity in Hippocampome.org.
(A) Subregional connectivity, where the number of connections between subregions is shown, and the node size is proportional to the number of neuron types in each subregion. (B) The reciprocal …
Figure 9
Spiking neural network simulations.
(A) Full-scale CA3 model. (A1) Neuron type connectivity schematic. (A2) Theta (4–12 Hz; top), Gamma (25–100 Hz; middle), and Sharp-Wave Ripple (150–200 Hz; bottom) filtered local field potentials …
Tables
Table 1
Added knowledge and functioning in Hippocampome.org releases v1.1–12.
| Version | Contribution | Article |
|---|---|---|
| v1.1 |
| Hamilton et al., 2017a |
| v1.2 |
| Rees et al., 2016 |
| v1.3 |
| Hamilton et al., 2017b |
| v1.4 |
| Moradi and Ascoli, 2020 |
| v1.5 |
| White et al., 2020 |
| v1.6 |
| Komendantov et al., 2019 |
| v1.7 |
| Venkadesh et al., 2019 |
| v1.8 |
| Tecuatl et al., 2021b |
| v1.9 |
| Sanchez-Aguilera et al., 2021 |
| v1.10 |
| Sutton and Ascoli, 2021 |
| v1.11 |
| Attili et al., 2022 |
| v1.12 |
| Moradi et al., 2022 |
Table 2
Probabilities of connection and number of contacts per connected pair from DG Granule cell to mossy fiber targets in CA3.
| Postsynaptic neuron type | Probability | # contacts |
|---|---|---|
| CA3 Pyramidal | 1.11E-04 | 1.08 |
| CA3c Pyramidal | 3.91E-04 | 1.31 |
| CA3 Spiny Lucidum Dentate-Projecting | 5.89E-04 | 1.69 |
| CA3 Mossy Fiber-Associated ORDEN | 4.44E-04 | 1.27 |
| CA3 Basket | 6.55E-04 | 1.50 |
| CA3 Basket CCK+ | 2.14E-04 | 1.16 |
| CA3 Ivy | 3.35E-04 | 1.29 |
| CA3 Mossy Fiber-Associated | 3.78E-05 | 1.04 |
| CA3 LMR-Targeting | 1.31E-04 | 1.21 |
| CA3 Lucidum ORAX | 2.62E-04 | 1.19 |
| CA3 Lucidum-Radiatum | 3.25E-04 | 1.13 |
| CA3 Axo-Axonic | 7.56E-04 | 1.50 |
| CA3 Bistratified | 8.25E-04 | 1.45 |
| CA3 QuadD-LM | 2.91E-04 | 1.25 |
Table 3
Examples of independent studies utilizing unique neuronal properties from Hippocampome.org v1.0.
| Article | Usage |
|---|---|
| Gulyás et al., 2016 | Lists of subthreshold physiological properties for multicompartmental modeling |
| Skene and Grant, 2016 | Catalog of CA1 Interneuron types |
| Faghihi and Moustafa, 2017 | Diversity of hippocampal neuron types and morphological neuronal features |
| Puighermanal et al., 2017 | Biomarker expression in CA1 interneurons |
| Depannemaecker et al., 2020 | Parameter values for a model of synaptic neurotransmission |
| Ecker et al., 2020 | Evidence that CA1 interneurons express multiple overlapping chemical markers |
| Hunsberger and Mynlieff, 2020 | Cell identification based on firing properties |
| Schumm et al., 2020 | Directionality of connections in the hippocampus |
| Aery Jones et al., 2021 | Local connectivity of CA1 PV + interneurons |
| Ciarpella et al., 2021 | Lists of hippocampal genes |
| Luo et al., 2021 | Confirmation of multiple hippocampal neuron types |
| Mehta et al., 2021 | Connectome model inspired by entorhinal-CA1 circuit |
| Obafemi et al., 2021 | Principal channels of information processing are DG Granule cells and CA1-3 Pyramidal cells |
| Sáray et al., 2021 | Membrane biophysics values for CA1 Pyramidal cells |
| Smith et al., 2021 | Omni-directionality of axons of CA1 Pyramidal cells |
| Venkadesh and Van Horn, 2021 | Example of a brain region’s mesoscopic structural connectivity |
| Walker et al., 2021 | Reference to morphological and molecular characteristics of hippocampal principal cells and interneurons |
| Wynne et al., 2021 | Example brain region with a variety of cell types |
| Kopsick et al., 2023 | Utilize accumulated knowledge as the basis for simulations |
| Schumm et al., 2022 | Hippocampal morphology, biomarker expression, connectivity, and typing of neurons |
| Zagrean et al., 2022 | Diversity of hippocampal neuronal types and their properties |
