Standarize Data Format

[TK-21st]

Neu3D currently handles loading data of a few formats, here we standardize the input data formats.

Input format

MorphologyData sent for multiple objects should be a dictionary with the rid of Morphology data as the key, and each value is a dictionary with the following fields:

• class: the type of data, e.g., 'Neuron', 'Synapse', 'Neuropil', etc.
• orid: the rid of the parent node,
• morph_type: the type of data and fields according to the morph_type.

MeshDict Object (output items in MeshDict)

• ffbo_json: {[rid:string]: data_to_be_loaded}
• type: 'morphology_json' | 'gltf' | string
• highlight: boolean
• visibility: boolean
• background: boolean
• color: THREE.Color | string (RGB hex)
• label: string
• colormap: string;
• colororder: 'random' | 'order;
• showAfterLoadAll: boolean;
• reset: boolean

if loading from file

• filename: string
• filetype: 'json' | 'swc' | 'syn' | 'gltf'

if loading from Obj

• dataStr: string

Morphology Transformations

The following attributes will be applied to all except gltf files.

• radius_scale = 1.
• x_scale = 1.
• y_scale = 1.
• z_scale = 1.
• x_shift = 0.
• y_shift = 0.
• z_shift = 0.
• xy_rot = 0.
• yz_rot = 0.
• xz_rot = 0.

Attributes added by _registerObject

• rid: string
• object: RenderObj
• pinned = false
• position: THREE.Vector3
• opacity: float

SWC (loadSWCCallBack)

Each row of the swcString is assumed to be a length-7 array with each item corresponding to the following entries

sample	type	x	y	z	radius	parent
int	int	float	float	float	float	int

type

• 0: undefined
• 1: soma
• 2: axon
• 3: (basal) dendrite
• 4: apical dendrite
• 5: custom
• 6: custom

parent = -1 indicates root

Mesh (loadMeshCallBack)

• vertices: Array
• faces: Array

MorphJSON (loadMorphJSONCallBack)

MorphJSON is assumed to be a json of 7 fields (as below) where each field is an array of corresponding items.

sample	identifier	x	y	z	r	parent
int	int	float	float	float	float	int

identifiers used for Neurons:

• 0: undefined
• 1: soma

Synapses need to take the special format to start listing all presynaptic sites with parent -1 and followed by postsynaptic sites using sample of its presynaptic sites as parent, e.g.	sample	identifier	x	y	z	r	parent
1	7	float	float	float	float	-1
2	7	float	float	float	float	-1
3	7	float	float	float	float	-1
4	8	float	float	float	float	1
5	8	float	float	float	float	2
6	8	float	float	float	float	3

GLTF (loadGltfCallBack)

• dataStr

[TK-21st]

@yiyin, related to my comment in #32, can you add in comments/edits to this issue?

[yiyin]

made some edits above

[TK-21st]

made some edits above

Great! Thanks! Will add this to a schema checker to object loader.

[yiyin]

Schema for MorphologyData (as of Neuroarch version 0.3.2)

'swc'

• x: list of double
• y: list of double
• z: list of double
• r: list of double
• parent: list of int
• sample: list of int
• identifier: list of int
• confidence: list of double (optional, for synapse only)

'mesh':

• faces: list of int, the first vertex is indexed as 0
• vertices: list of double, the length should be 3 times the number of vertices , e.g., [v[0].x, v[0].y, v[0].z, v[1].x, v[1].y, v[1].z, ...]

'obj'

not currently defined

[TK-21st]

Thanks @yiyin! Closed by 1a01f9450c0b46a6e2bf4fcd8b62dd97e9033520