Introduction

About

Microanalyst is both a Python module and a set of utility scripts for the analysis and visualization of data acquired with Tecan® i-control™ microplate reader.

Motivation

The original experiment which led to the inception of this project was held at the Institute of Environmental Sciences of the Jagiellonian University.

The goal of the experiment was to determine genes whose expression gives a strong effect on survival of non-dividing cells in a repeatable manner.

There were around 6,000 yeast strains (Saccharomyces cerevisiae) with different sets of genes. Yeast extinction and survival would be observed by keeping the samples in a carbon-free environment. The entire collection of 65 microplates (8 rows by 12 columns each) was measured at roughly two-weeks time intervals and repeated in a few redundant series.

Microplates

  • There were 65 microplates in the whole experiment.
  • Each microplate had a unique name.
  • Each microplate consisted of 96 wells with samples.
  • Wells were arranged in 8 rows denoted with letters [A-H] and 12 columns denoted with numbers [1-12].
  • Some microplates did contain empty control wells, whose presence and location had been determined by the manufacturer upfront.

Spreadsheets

  • Microplates were scanned with a Tecan® Infinite® 200 reader device, which produced .xls files (Microsoft® Excel™).
  • A single Excel™ document could contain readouts taken over a period of multiple days, although typically there would be a one-to-one relationship, i.e. one Excel™ file per day.
  • It took approximately 40 seconds to scan one microplate.
  • The readout of a single microplate included the following:
    • name of the microplate
    • date and time
    • temperature in Celsius degrees (usually around 30 degrees)
    • 96 floating point values (e.g. associated with the absorbance - optical density - at a particular wavelength and bandwidth)
  • Name of an Excel™ sheet coincided with the corresponding microplate name.
  • Additional sheets with metadata were ignored.
  • Excel™ sheets were stored in no particular order.

Interpretation

  • Values below 0.2 were considered starvation of a sample.
  • Values above 0.8 were most likely an unwanted infection.
  • Values above 0.06 in a control well also indicated a high probability of an infection in the microplate since that is the absorbance of the material comprising the microplates.