Blue Blob Detection

Contents:

• Blue Blob Detection
  • Introduction
  • Prerequisites
  • Run it
  • Matlab and Python integration
    • Prerequisites
    • Matlab Code

Introduction

This script aims to detect blue blobs that represent center of cells of an organic tissue.

A Voronoi diagram is drawn over these detected blue blobs in order to represent the cells themselves.

Finally, we would like to simulate a blood flow in animating this diagram by giving a speed to the cells coming from a speed field.

WARNING

The detection is working only if the blobs are blue and nothing else. It cannot be use for doing a General Blob Detection !

Prerequisites

For the "Computer Vision", the script uses OpenCV library we choose to use for its efficiency:

OpenCV For Linux

OpenCV For windows

Run it

Please, check the script's options if you are interested in specifying the parameters of the detection :

python bbd.py -h

which should gives you :

You can try a first detection by using the image organic.tif :

python bbd.py -i images/organic.tif

The processed image organic_processed should be generated and you should see the following stdout :

You can modify some parameters like the connectivity of the detection, the color of the Voronoi diagram etc...

Matlab and Python integration

Prerequisites

In order to be able to execute the Python script from Matlab, you have to :

Install Matlab API for Python

Add the git folder Blue-Blob-Detection containing bbd.py script to the PythonPath :

Add a path to PythonPath in Windows

Add a path to PythonPath in Linux

Matlab Code

python_return_value = py.bbd.main('ABSOLUTE_PATH_OF_THE_IMAGE\images\organic.tif');
python_arrays = python_return_value{1};

facets_number = size(python_arrays, 2);
matlab_cell = cell(facets_number,1);

for i = 1:facets_number
	temp_array = python_arrays{i};
	matlab_cell{i} = double(py.array.array('d',py.numpy.nditer(temp_array)));
end

matlab_cell variable should contain a list of coordinates for each polygone of the Voroinoi diagram which can be use in the simulation model of organic cells developed at Centre Universitaire d'Informatique.