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Worm movement assay
Jupyter Notebook Python
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NIS_elements_example_script.xml
README.md
example_data_analysis.ipynb
example_levamisole_data.npy
export_nd2.py
quantify_movement.py
quantify_movement_adult.py

README.md

acute_assay

Supporting information for "An image-based assay for the rapid quantification of C. elegans movement in response to genetic and chemical perturbations"

Overview

The files here should be sufficient to reproduce the data acquisition and analysis pipeline described in our paper, used in conjunction with several other packages of freely-available software.

The files are:

File Description
NIS_elements_example_script.xml An example microscope control macro for use in Nikon NIS elements sortware
export_nd2.py Custom python script to extract individual 8-bit TIFF images from Nikon ND2 files
quantify_movement.py Custom python script to analyse a set of 8-bit image files from an experiment, return mobility scores
quantify_movement_adult.py As above but tuned for larger, adult worms. Ignores eggs in the well
example_levamisole_data.npy numpy array containing sample FMS data for a range of levamisole concentrations
levamisole_analysis.ipynb An example jupyter (formerly ipython notebook) file illustrating normalization and plotting of data

Required third-party software:

  1. Python 2.7
  • numpy
  • scipy
  • matplotlib
  • scikit-image
  1. ImageMagick (for export_nd2.py): https://www.imagemagick.org/script/index.php
  2. bfconvert: http://www.openmicroscopy.org/site/support/bio-formats5.4/users/comlinetools/
  3. Jupyter: http://jupyter.org/

Example Data

A set of example images is available at Open Science Framework: https://osf.io/p372e/

Running quantify_movement.py on the example images should recreate the fractional mobility score data in example_levamisole_data.npy

An example jupyter notebook, levamisole_analysis.ipynb illustrates the normalization of data and plotting procedure, using the data in example_levamisole_data.npy.

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