/growth-profiler-align

Primary LanguagePython

Growth Profiler Image Analyzer

This package contains functions for analysing the raw image outputs of the growth profiler.

Installation

Installing Python

Skip this if you already have a working installation of Python. To use this package you need to have Python. Using the operating system's built-in Python interpreter is not recommended. The easiest way to obtain Python is from https://www.continuum.io/downloads - Select the relevant OS and download the Python 3.X installer (Python 2.7 will also work for now, but Python 3 is recommended). - Run the installer and follow the instructions. - Open a terminal (windows: search for 'command prompt'/'cmd.exe', OSX/Linux: search for 'terminal') in your operating system and type python -V. This should print the version of Python, and contain the word 'Anaconda'

Installing the Growth Profiler Image Analyzer (gpalign)

Installation is as easy as running the following line of code in your terminal (Anaconda or other Python environment).

$ pip install https://github.com/biosustain/growth-profiler-align/archive/master.zip

This will install all necessary requirements as well as the gpalign command line program.

Usage

You can find useful information in the help of the gpalign program and its subcommands.

$ gpalign -h
$ gpalign analyze -h
$ gpalign convert -h

Analyzing the Images

  • Navigate to the directory where you want the output files to be placed. Make sure this is a location where you have permission to create files, e.g., a subdirectory of Documents.

  • Figure out which plate type was used for the run and use the number in the subsequent commands:

    • Black 96 well (<plate type>=1)
    • White 96 well (<plate type>=2)
    • White 24 well (<plate type>=3)

  • To analyse the plates run the following code filling in the parameters:

    $ gpalign analyze --scanner <1 or 2> --plate_type <plate type> --out <base path> "<terminal pattern for images>"

  • To analyse the plates in scanner 2, for example, run

    $ gpalign analyze --scanner 2 --plate_type 2 --out Profiles/scanner_2 "Images/Scanner 2/*.Png"

  • The output files will have _trayX.G.tsv appended to the output path. For the above example: Profiles/scanner_2_tray1.G.tsv and so on. The below table shows how the trays are organised in the scanners.

  • N.B.: You should place your plates such that A1 is in the upper right corner. Otherwise you should add the argument --orientation bottom-left to the above commands.

  • You can choose to analyse individual plates only by specifying the

--trays parameter one or more times:

$ gpalign analyze --scanner 2 --plate_type 2 --trays 7,10 --out Profiles/scanner_2 "Images/Scanner 2/*.Png"

Tray Layouts

Scanner 1
1 4
2 5
3 6
Scanner 2
7 10
8 11
9 12

Converting the G-values to OD

  • Obtain a set of calibration parameters (A, B, C) from Kristian
  • Run gpalign convert A B C "<terminal pattern>"