plaque-size-tool 1.0.2

Bacteriophage plaque size measurement tool

Bacteriophage plaques size tool

This Python 3 tool takes Petri dish images as input and measures the sizes of the bacteriophage round and oval-shaped plaques.

Installation

Installation using pip

The following command should be executed:

pip install plaque-size-tool

Upgrade using pip

Upgrade an already installed package to the latest from PyPI:

pip install --upgrade plaque-size-tool

Prerequisites

1. Python 3.6 or higher should be installed in the system:

   For Python 3 installation, please navigate to https://www.python.org/downloads/. The detailed instructions for download and installation are provided at https://wiki.python.org/moin/BeginnersGuide/Download.

2. PIP should be installed in the system:

   pip is already installed if you are using Python 2 >=2.7.9 or Python 3 >=3.4 downloaded from python.org. If it is not installed, please navigate to https://pip.pypa.io/en/stable/installing/ for the instructions.

By default the tool will be installed into the directories depending on the OS:

Please see https://docs.python.org/3/install/ for the details.

Usage

The tool supports TIF, TIFF, JPG, JPEG and PNG image formats.

Run the tool

To run the tool, use one of the following options. The output will be placed into ./out directory of the project.

on a file

If it's required to analyze a single file, run the following command:

python plaque_size_tool.py -i <path_to_the_file> [-p plate_size] [-small]

on a directory

If it's required to analyze multiple files, put all files in the directory. Then run the following command:

python plaque_size_tool.py -d <path_to_the_directory> [-p plate_size] [-small]

Additional options

-p plate_size - (Optional) Petri dish size (mm). If not specified all measurements are taken in pixels.
-small - (Optional) Use on plates with small plaques (less than 2.5 mm) 

##Examples

python plaque_size_tool.py -i Test_plates/large/29.tif -p 90
python plaque_size_tool.py -i Test_plates/small/7.tif -p 90 -small

Output

The tool produces two output files:

1. out_<file_name> - an image with valid plaques circled with green colour, where <file_name> is the name of the original file

2. data-green-<file_name>.csv - a CSV file with detected plaques parameters: 
INDEX_COL - the ID of the plaque that corresponds to the ID on the output image
AREA_PXL - Area of a plaque in pixels
PERIMETER - Perimeter of a plaque in pixels
AREA_MM2 -  Area of a plaque in millimiters if plate size is specified
AREA_MM2 -  Area of a plaque in millimiters squared if plate size is specified
DIAMETER_MM - Diameter of a plaque in millimiters if plate size is specified    

Notes

This tool was tested on grey images in TIF format made using a Bio-Rad GelDoc system with the Exposure parameter equal to 0.750 sec. The tool can automatically adjust brightness and contrast of images for processing. If you are experiencing any issues with your images (for example, overprocessing), please email to [e-mail] with a copy to [e-mail]