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Flynotyper — Mon, 02 Mar 2015 16:02:28 -0000

Flynotyper 1.0

Introduction

This software is to quantify phenotypes in Drosophila by detecting arrangement as well as
fusion events in the ommatidia. The eye system in Drosophila melanogaster has proven to be
an extremely valuable genetic screen in Drosophila genetic studies. However, there lacks a
simple and inexpensive method, which allows reliable quantification of the eye phenotypes
in a high-throughput manner. Our method used in this application provides a powerful
screening system for developmental genes in Drosophila melanogaster. We utilizes ommatidia
count and arrangements to rapidly quantify genetic screens using eye images produced by
both compound microscopes and scanning electron microscope (SEM). We tested this method
in different RNAi lines.

System Requirements

Flynotyper depends on the OpenCV library
for image processing. Version 2.4.10+ is preferred. To install OpenCV, your system will
also need GCC 4.4.x or later, and CMake 2.6 or higher. Please install OpenCV and its
dependencies by following the instructions in the "Installation" section.

Installation

Install OpenCV

Make sure you have GCC and CMake installed on your system.
Download the latest version of OpenCV:
bash $ cd ~/<my_working_directory> $ git clone https://github.com/Itseez/opencv.git

Build OpenCV

bash $ cd ~/<my_working_directory> $ mkdir build $ cd build $ cmake -D CMAKE_BUILD_TYPE=Release -D CMAKE_INSTALL_PREFIX=/usr/local .. $ make $ sudo make install
The full instruction for the installation of OpenCV can be found at this link

Build flynotyper

Download the source code: [flynotyper.tar.gz] ()
bash $ tar -vxf flynotyper.tar.gz $ cd flynotyper $ make
Copy flynotyper to a location you want (e.g. a directory in your $PATH).

Usage

Run the program by using the filename of the eye image as the input and different parameters:
bash $ flynotyper <filename> [-sem] [-n count]

parameters:
bash -sem: use this parameter when the image file was taken by SEM. -n count: the number of most stable ommatidia taken into consideration when calculating the phenotypic score (see the paper for more detailed information). The default number is 200.

For example, to get the phenotypic score for the image eye.tif in the "example" folder, run:
bash $ flynotyper eye.tif

If the image was taken by the SEM, use parameter -sem after the file name.

For eample, to get the phenotypic score for the image sem.tif in the "example" folder, run:
bash $ flynotyper sem.tif -sem

Output

The output includes 5 columns, which will be as the following example:

Ed	Ea	E	Z	P
334.334	588.983	294.491	575	46.3446

In which:
Ed: Total distance entropy of all stable ommatidia;
Ea: Total angel entropy of all stable ommatidia;
E: Total entropy of all stable ommatidia, E = Ed + Ea;
Z: Fusion index, which is the number of detected ommatidia;
P: Phenotypic score, calculated based on E and Z.

The more detailed information about the result could be found in our paper.

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Flynotyper — Mon, 02 Mar 2015 15:36:06 -0000

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