Welcome to brain_diffusion

brain_diffusion is a python library designed to analyze and visualize trajectory data from the ImageJ plugin MOSAIC.

Usage

import brain_diffusion.msd as msd

DIR = '../data/'
file = 'sample_data'

# Prepare trajectory file
total, frames, x, y, xs, ys = msd.MSD_iteration(DIR, file)

# Calculate mean squared displacements and their geometric averages
geoM2xy, gSEM, SM1x, SM1y, SM2xy = msd.vectorized_MMSD_calcs(frames, total, xs, ys)

Motivation

Mean squared displacement (MSD) calculations are a standard calculation performed by scientists and researchers who use multi-particle tracking techniques. Brain_diffusion is a centralized analysis and visualization package to calculate MSDs and diffusion coefficients from trajectory data as calculated using the MOSIAC ImageJ plugin developed by in the MOSAIC Group at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden. This calculation package is the primary tool for MSD calculations of nanoparticles in the brain in the Nance research group at the University of Washington.