Rewired connectome of an SSCX model with inhibitory targeting based on trends found in MICrONS data
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1.
École Polytechnique Fédérale de Lausanne
Description
This is a rewired connectome of the internal synaptic connectivity of the model deposited under https://zenodo.org/records/7930275.
In the original model, local connectivity is based on axo-dendritic overlaps combined with a pruning rule, which together are known to be able to recreate biological trends in excitatory subnetworks. By comparison with the MICrONS dataset we found that the inhibitory trends characterized by Schneider-Mizell et al. (2023) can be reproduced with some additional, relatively simple pruning rules (see accompanying anatomy publication), and created a rewired version of the connectome in SONATA format (edges.h5) that reproduces these trends. We refer to this as the Schneider-Mizell compatible SM-connectome in the accompanying physiology publication.
Note that for technical reasons, all afferent_segment_... and efferent_... synapse properties (which are not required for running simulations) were set to zero in the rewired pathways.
[Update 08/05/2024 - v3]: Conductances of individual synapses were recalibrated to preserve pathway-specific reference PSP amplitudes. The afferent_section_type and efferent_section_type synapse properties were previously off by 1 and were fixed. Missing synaptic input compensation was recalibrated to obtain target firing rates and added to this release.
[Update 28/02/2024 - v2]: Source m-type L1_NGC-SA included
Notes
- Uncompress edges.h5:
tar -xf edges.xz - Replace original edges.h5 by extracted file
For running simulations:
- Follow simulation instructions from our full model release
- Use exemplary simulation configurations for different spontaneous states with recalibrated input compensation that are included in this release (spontaneous_activity_simulation.zip)
Technical info
Numbers of connections and synapses in the rewired vs. the original connectome
- Overall:
| Original | Rewired | Difference | Difference (%) | |
| Number of connections | 87,457,567 | 115,160,718 | 27,703,151 | 31.68% |
| Number of synapses | 407,127,134 | 406,836,913 | -290,221 | -0.07% |
- Rewired pathways only:
| Original | Rewired | Difference | Difference (%) | |
| Number of connections | 3,840,617 | 31,543,768 | 27,703,151 | 721.32% |
| Number of synapses | 56,669,829 | 56,379,608 | -290,221 | -0.51% |
Rewired pathways: 26 (inhibitory) source m-types to all (excitatory/inhibitory) target m-types
Additional details can be found in the supplementary document Zenodo___Rewired_SSCX_with_inhibitory_trends_from_MICrONS__v3.pdf.
Files
Zenodo___Rewired_SSCX_with_inhibitory_trends_from_MICrONS__v3_.pdf
Additional details
Related works
- Is derived from
- Dataset: 10.5281/zenodo.8026353 (DOI)