ZebIAT: Zebrafish Image Analysis Tool

News

Version 1.00

About

ZebIAT is a tool for registering zebrafish images acquired by fluorescence microscope as well as differential interference microscope. The tool offers automatic and semi-automatic methods to analyze images and thus allow, e.g. quantitative comparisons between images. The tool uses a thin plate splines registration method.


Reference: T. Annila, E. Lihavainen, I.J. Marques, D.R. Williams, O. Yli-Harja and A.S. Ribeiro. 2013. ZebIAT, an image analysis tool for registering zebrafish embryos and quantifying cancer metastasis. BMC Bioinformatics 14 (Sup. 10), S5, in press.

Download

Matlab source code can be downloaded here:

MATLAB source code

Zebratool requires also some addition files in order to work. For spot detection we used wavelet segmentation algorithm based on article "Ruusuvuori et al.: Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images". For interpolation we used "inpaint" technique which can be downloaded from Mathworks:

"Inpaint"-method
"Atrouswave"-method for spot detection

We also provide a set of fluorescence microscope images of zebrafish for testing. The guide for using the tool is also provided.

Example images
Userīs manual

Contact


Andre Ribeiro
andre.ribeiro (at) tut.fi

Links

The MathWorks - For information about MATLAB