Skip to content
Python wrapper for running Vaa3d functions
Python
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
pyVaa3d
tests
.gitignore
INSTALL.md
LICENSE
MANIFEST.in
README.md
setup.py

README.md

pyVaa3d

Python wrapper for running Vaa3d functions

Features:

  1. A method that is equivalent of running a specific function of a specific plugin of vaa3d (essentially, vaa3d -i <...> -x <...> -f <...>). It returns printed output on stdout.
  2. Convenience method to generate all global features of neurons, specified using a SWC files, and returning features as pandas tables.
  3. Python 2/3 support
  4. Linux, MacOS and Windows support
  5. Unit testing

Limitations:

  1. Works only with Vaa3d v3.447

Installation

See the file INSTALL.md

Example Usages

Basic commandline functionality

Here we call the function "tracing_func" of plugin "EnsembleNeuronTracerV2s" on the file "input.tiff". This plugin reconstructs neuron morphology from "input.tiff" using the "EnsembleNeuronTracerV2s" plugin.

from pyVaa3d.vaa3dWrapper import runVaa3dPlugin
runVaa3dPlugin(inFile=inFile, pluginName="EnsembleNeuronTracerV2s",
                   funcName="tracing_func")

Computing Global features of SWC morphologies

Global neuron features are calculated for the SWC morphologies "1.swc" and "2.swc" and save it to the excel file "GlobalNeuronFeatures.xlsx".

from pyVaa3d.global_neuron_features import getGlobalNeuronFeatures
swcFiles = ["1.swc", "2.swc"]
outDF = getGlobalNeuronFeatures(swcFiles)
outDF.to_excel("GlobalNeuronFeatures.xlsx") 
You can’t perform that action at this time.