KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, Peptides, and Recombinant Proteins
Paraformaldehy de, 16% aqueous solution	Electron Microscopy Sciences	cat.#15710, CAS: 30525-89-4
Glutaraldehyde, 25% aqueous solution	Electron Microscopy Sciences	cat.#16220, CAS: 111-30-8
Osmium tetroxide, 4% aqueous solution	Electron Microscopy Sciences	cat.#19190, CAS: 20816-12-0
Potassium ferricyanide	Sigma Aldrich	CAS: 13746-66-2
Thiocarbohydraz ide	Sigma Aldrich	223220, CAS: 2231-57-4
Hard Plus Resin - 812	Electron Microscopy Sciences	cat.#14115
0.2M Sodium cacodylate buffer	Electron Microscopy Sciences	cat.#11652
Uranyl acetate	Polyscienc es	cat.#21447-25
L-aspartic acid	Sigma Aldrich	CAS: 45ZU62
Lead nitrate	Electron Microscopy Sciences	CAS: 10099-74-8
Deposited Data
Electron microscopy image volume	This paper	layer23.microns-explorer.org
Morphological segmentation	This paper	layer23.microns-explorer.org
Synaptic cleft segmentation	This paper	layer23.microns-explorer.org
Mitochondrion segmentation	This paper	layer23.microns-explorer.org
Cellular nucleus segmentation	This paper	layer23.microns-explorer.org
2-Photon calcium traces	This paper	microns-explorer.org/phase1
Deconvolved spike estimates and tuning curves	This paper	github.com/seung-lab/datajoint_seung
Light Microscopy coregistration volume	This paper	github.com/AllenInstitute/MicronsBinder/tree/master/notebooks/vignette_an alysis/function
Synaptic connectivity tables	This paper	https://zenodo.org/record/5579388
PyC-PyC connectivity graph	This paper	https://zenodo.org/record/5579388
Cell classification table	This paper	https://zenodo.org/record/5579388
Mitochondrion information table	This paper	https://zenodo.org/record/5579388
Nucleus information table	This paper	https://zenodo.org/record/5579388
Cell skeletons used for analysis	This paper	https://zenodo.org/record/5579388
Cell triangle meshes used for analysis	This paper	https://zenodo.org/record/5579388
Analysis intermediate data (see MicronsBinder)	This paper	https://zenodo.org/record/5579388
Experimental Models: Organisms/Strains
Mouse line: Cre driver: CamKIIa-Cre	Jax	jax.org/strain/005359
Mouse line: tTA driver: B6;CBA- Tg(Camk2a-tTA)1Mmay/J	Jax	jax.org/strain/003010
GCaMP6f Reporter: Ai93	Allen Institute for Brain Science	jax.org/strain/024103
Software and Algorithms
Python 3	Python.org	python.org
Reconstruction source code	This paper	github.com/seung-lab/microns-L23-reconstruction; doi:10.5281/zenodo.5851066
Data analysis source code	This paper	github.com/AllenInstitute/MicronsBinder; doi:10.5281/zenodo.5856928
Alembic	MICrONS Consortium	github.com/seung-lab/Alembic
TrakEM2	(Cardona et al., 2012)	ini.uzh.ch/~acardona/trakem2.html
Render	(Zheng et al., 2018)	github.com/saalfeldlab/render
VAST	(Berger, Seung and Lichtman, 2018)	lichtman.rc.fas.harvard.edu/vast/
PyTorch	(Paszke et al., 2019)	pytorch.org
ChunkFlow	(Wu et al., 2021)	github.com/seung-lab/chunkflow
zmesh	MICrONS Consortium	github.com/seung-lab/zmesh
PyChunkedGraph	(Dorkenwald et al., 2020)	github.com/seung-lab/PyChunkedGraph
Kimimaro: Densely Labeled Image Skeletonization	MICrONS Consortium	github.com/seung-lab/kimimaro
Igneous	MICrONS Consortium	github.com/seung-lab/igneous
MeshParty	MICrONS Consortium	github.com/sdorkenw/MeshParty
EASE	(Zhou et al., 2020)	github.com/zhoupc/ease
DataJoint	Vathes LLC	datajoint.com
Scipy: Fundamental Algorithms for Scientific Computing in Python	(Virtanen et al., 2020)	scipy.org
Seaborn: statistical data visualization	(Waskom, 2021)	seaborn.pydata.org
Statsmodels: Econometric and statistical modeling with python	(Seabold and Perktold, 2010)	statsmodels.org
Neuroglancer	Google	github.com/google/neuroglancer
ParaView	National Technology & Engineering Solutions of Sandia, LLC (NTESS), Kitware Inc.	paraview.org
MeshLab	Visual Computing Lab, ISTI, Consiglio nazionale delle ricerche (Cnr)	meshlab.net