neat.MorphTree.readSWCTreeFromFile

MorphTree.readSWCTreeFromFile(file_n, types=[1, 3, 4])[source]

Non-specific for a “tree data structure” Read and load a morphology from an SWC file and parse it into an neat.MorphTree object.

On the NeuroMorpho.org website, 5 types of somadescriptions are considered (http://neuromorpho.org/neuroMorpho/SomaFormat.html). The “3-point soma” is the standard and most files are converted to this format during a curation step. neat follows this default specification and the internal structure of `neat` implements the 3-point soma. Additionally multi-cylinder descriptions with more than three nodes are also supported, but are converted to the standard three point description.

Additionally, the root node of the tree must have index == 1, swc_type == 1 and occur first in the SWC file.

Parameters

  • file_n (str) – name of the file to open

  • types (list of ints) – NeuroMorpho.org segment types to be loaded

Examples

The three point description is

1 1 x y   z r -1
1 1 x y-r z r 1
1 1 x y+r z r 1

with x,y,z the coordinates of the soma center and r the soma radius

This is a valid three point desciption

# start of file
1 1 45.3625 18.6775 -50.25 10.1267403895 -1
2 1 45.3625 8.55075961052 -50.25 10.1267403895 1
3 1 45.3625 28.8042403895 -50.25 10.1267403895 1
# dendrite nodes
4 3 37.76 12.99 -46.08 0.29 1
5 3 26.7068019951 8.26344199599 -36.9426896493 0.795614809475 4
# ...

This is a valid multi-cylinder descirption

# start of file
1 1 1066.38 399.67 157.0 4.9215 -1
2 1 1071.3 399.67 157.0 4.9215 1
3 1 1076.22 399.67 157.0 4.9215 2
4 1 1066.5 402.83 157.0 11.494 2
5 1 1062.4 405.5 157.0 15.308 4
6 1 1056.6 410.25 158.0 20.536 5
7 1 1056.6 410.25 158.0 20.536 6
8 1 1070.0 427.75 161.0 2.305 7
# dendrite nodes
9 3 1070.0 427.75 161.0 0.886 8
# ...
Raises

ValueError – If the SWC file is not consistent with the aforementioned conventions