EM derived morphology of 50k neurons from mouse visual cortex: Synapse and morphology data of a neuron in a P87 male mouse

[ DOI: https://doi.org/10.35077/add-own ]

 

Dataset Citation:

Reid, Clay, MiCONS Consortium-IARPA, Joyce, Emily, Collman, Forrest, Schneider-Mizell, Casey. (2023). EM derived morphology of 50k neurons from mouse visual cortex: Synapse and morphology data of a neuron in a P87 male mouse. [ Dataset / Microscopy ]. Brain Image Library. https://doi.org/10.35077/add-own

 

Abstract:

3D anatomical reconstruction and synapse map of neuron in mouse visual cortex obtained from serial section Electron Microscopy imaging from the IARPA MICrONS dataset. More information on the can be found on MICrONS Explorer https://www.microns- explorer.org/cortical-mm3. Most of the included h5, json and swc files represent dendrite and soma morphologies of excitatory neurons that have been automatically reconstructed with little to no human proofreading. These span much of the millimeter cubed of the MICrONS dataset except for the edges where the majority of the morphology would be cut off. There is a smaller subset of human proofread excitatory and inhibitory neurons with axons, dendrite and soma reconstruction. This information is accessible in the json files. h5 files here can be ingested into a meshwork object in python with the package MeshParty https://github.com/sdorkenw/MeshParty. This meshwork integrates anatomical data and other user defined annotations such as synapses. The meshworks here contain annotation tables including pre and post synaptic chemical synapses on the given neuron and the ids of the post or presynaptic neurons respectively. Unless the neuron has had a high level of proofreading, the axon has been masked and removed. json files contain metadata and morphological features of the neuron skeleton including the proofreading version of the MICrONS dataset, the various ids of the given body, and lenghts of certain compartments. More information on the contents of this filetype can be found on the MicRONS explorer skeleton page.

 

Methods:

Please see README.xlsx for more information.

 

TechnicalInfo:

DATASET METADATA:
title	EM derived morphology of 50k neurons from mouse visual cortex: Synapse and morphology data of a neuron in a P87 male mouse
socialMedia	Synapse and morphology data of a neuron in a P87 male mouse visual cortex
Subjectscheme	soma and root ids for IARPA MICrONS neurons. Ids tied to tables from CAVE (Connectome Annotation Versioning Engine)
GeneralModality	connectivity
Technique	other
Other	anatomical data derived from serial section EM image stack
SPECIMEN METADATA:
LocalID	M180517
Species	Mouse
NCBITaxonomy	NCBI:txid10090
Age	87.0
Ageunit	Days
Sex	Male
Genotype	SLC17a7-Cre
;Reporter_Name='Ai162';'OrganName	Brain
SampleLocalID	M180517
Atlas	AllenMouseV2
Locations	VIS - Visual cortex
INSTRUMENT METADATA:
MicroscopeType	Electron Microscope
MicroscopeManufacturerAndModel	JEOL 1200EXII 120kV TEM
ObjectiveImmersion	Oil
DetectorType	CMOS
DetectorModel	Ximea CB500MG-CM
IlluminationWavelength	400–850 nm
IMAGE METADATA:
xAxis	NA
yAxis	NA
zAxis	NA
Number	NA
displayColor	NA
stepSizeX	NA
stepSizeY	NA

 

Funding:

National Institutes of Health 1-RF1-MH125932-01A1 From synapses to genes through morphology: an integrated characterization of cell types based on connectomics and transcriptomics data;
Office of the Director of National Intelligence D16PC00004 Intelligence Advanced Research Projects Activity: Machine Intelligence from Cortical Networks;
National Science Foundation 2014862.0 NeuroNex2: Enabling Identification and Impact of Synaptic Weight in Functional Networks

 

Contributors:

Reid, Clay (ProjectLeader) [ORCID: https://orcid.org/0000-0002-8697-6797 ] Allen Institute for Brain Science
MiCONS Consortium-IARPA (ResearchGroup) Office of the Director of National Intelligence
Joyce, Emily (DataCurator) [ORCID: https://orcid.org/0000-0001-5794-6321 ] Allen Institute for Brain Science
Collman, Forrest (DataCurator) [ORCID: https://orcid.org/0000-0002-0280-7022 ] Allen Institute for Brain Science
Schneider-Mizell, Casey (DataCurator) [ORCID: https://orcid.org/0000-0001-9477-3853 ] Allen Institute for Brain Science

 

Related Identifiers:

IsCitedBy [ DOI : https://doi.org/10.1101/2021.07.28.454025 ];

 

Data location on the Brain Image Library Analysis Ecosystem:

/bil/data/6a/dc/6adc92187b04d98e

 

Dataset Download Link:

[ https: https://download.brainimagelibrary.org/6a/dc/6adc92187b04d98e]