File formats

Format	Content	Writer / reader	Spec
Project JSON (+ .npz sidecar)	geometry, fields, schedule, genome, plan, plugins, neuron model	neurogenesis.project.Project	Project Format (Schema Version 1.0.0)
Network JSON	neurons and synapses of an SNNNetwork	net.save_json, SNNNetwork.load_json	readable; for small and medium networks
NGB1	binary network: int32 indices, float64 positions, optional extension columns	neurogenesis.bridge.ngb	Bridge protocol, version 1.0 (section 6)
Module JSON (neurogenesis-module/1)	plan, genome, interface, validation, provenance	Module.save, Module.load	Tutorial 8 — Modules: share and compose circuits
Genome JSON	genome with "src->dst" projection keys	neurogenesis.genome.to_json, from_json	Core concepts
CSR arrays	row_ptr, col_idx, weights, delays	net.to_csr()	kernels
SONATA	nodes / edges HDF5, type tables, circuit config, for BMTK, NEST, NEURON, libsonata	neurogenesis.interop (export_network(net, "sonata", dir), import_network)	Running grown networks in other simulators
SWC	neuron morphologies (skeletons)	neurogenesis.arbors.read_swc, write_swc; connectome skeletons with simplification: neurogenesis.data.skeletons	Stage, geometry and field reference (arbors)

Exchanging networks

from neurogenesis.spiking.network import SNNNetwork
net = SNNNetwork.load_json("network.json")
row_ptr, col_idx, weights, delays = net.to_csr()          # NumPy arrays (presynaptic rows)

The CSR arrays can be loaded into SciPy (scipy.sparse.csr_matrix((weights, col_idx, row_ptr))), NetworkX or any graph library.

PLACEHOLDER

Further formats (roadmap phase J): NIR, PyNN scripts, NeuroML 2 / LEMS (Gleeson et al. 2010), gene-expression atlas grids as fields, NWB / neo recordings as fitting targets.