Supporting information for "An image-based assay for the rapid quantification of C. elegans movement in response to genetic and chemical perturbations"
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:
- Python 2.7
- numpy
- scipy
- matplotlib
- scikit-image
- ImageMagick (for export_nd2.py): https://www.imagemagick.org/script/index.php
- bfconvert: http://www.openmicroscopy.org/site/support/bio-formats5.4/users/comlinetools/
- Jupyter: http://jupyter.org/
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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