View and analyse data from the cell-free chemostats at LBNC.
This script analyses sequential timelapse images. The signal appears as fluorescence within a microfluidic channel, which is used to rotate and centre the image stack. ROIs are defined in the bright and dark regions, and intensities averaged within them. The script produces timeseries data of fluorescence intensity for each microchemostat reactor as well as merged images and plots. Analysis of a calibration experiment determines the dilution rate within each reactor. This code is used to analyse experiments run on chips as described in Niederholtmeyer et al. 2013 and Niederholtmeyer et al. 2015.
To install dependencies, run
pip install -r requirements.txt
There are three files:
cellfreeanalysis.py, the main scriptfunctions.py, which contains all the function definitions required by the main scriptconfig.py, which is used to set analysis parameters
Running the code generates *.csv output data files, *.pdf plots and images, and *.txt log files. These are directed to an output directory as defined within the config file.