Ostd Format Usage

This document shows how to use the ostd format implementation. See SPEC.md for controlling information on how to create or parse a file.

Python

Most people will want to create a osteoid.Skeleton obect by reading or writing an ostd file just like they would with an SWC.

import osteoid
skeleton = osteoid.load("example.ostd")
skeleton.save("example.ostd")

However, there is information in OSTD headers that could be parsed without reading in the entire file.

from osteoid.formats.ostd import OstdSkeleton

skeleton = OstdSkeleton.load("example.ostd", allow_mmap=True)
skeleton.cable_length
skeleton.num_components
skeleton.num_vertices
skeleton.num_edges

CLI

You can read and convert .ostd files with the ostd command line tool.

ostd info example.ostd # prints header and some attribute info

Convert between formats:

ostd convert example.swc example.ostd
ostd convert example.ostd example.swc

You can even view a skeleton:

ostd view example.swc
ostd view example.osdt