Analysis of data from plate readers

The analysis code is written in Python and uses the NumPy, SciPy, Matplotlib and Pandas modules. I like the Anaconda package, which is straightforward to install and includes IPython and BioPython as well.

All the analysis code is in our GIT repository on skye under PythonScripts. You will need five files:

  platereader.py
  gaussianprocess.py
  fitderiv.py
  genutils.py
  ODcorrection_Glucose_Haploid.txt

The software will directly load either an .xls or .xlsx file created by the platereader, but an additional file describing the contents of the wells is necessary (here is an example).

Each well should be labelled as "strain in media", such as "GAL1 in 2% Raf". Control wells that contain only media are labelled as "null" in media, such as "null in 2% Raf". Wells can left blank if either empty or contaminated.

There are detailed instructions for the data analysis.