Main window of MicrobeTracker

MicrobeTracker is a MATLAB-based program designed to detect and outline bacterial cells in images obtained by light microscopy and to analyze fluorescence signal inside them. The program generally requires phase contrast images for the analysis, though in some cases they may be replaced with fluorescence images, e.g. with diffuse fluorescent proteins, or with DIC images that have to be converted to symmetric (phase contrast-like) representation using a tool included in a separate file. When applied to individual images, MicrobeTracker combines traditional thresholding technique with morphological opening operations and edge detection to obtain the initial guess of the shape. Then this shape is additionally Fourier-smoothed and may be refined using one of a few more complicated techniques, including versions of Active Contour and Point Distribution Model (PDM).

Detected cells are saved in the form of 'meshes', which provide a coordinate system along the cell. The meshes alone can be used to measure the cell diameter and its uniformity, and to determine cell length, volume, curvature and other geometrical parameters. In combination with fluorescence images, the program can be used to determine the profile of the signal along the cell. This signal provides the total intensity and relative intensity of individual fluorescence foci or polarity of localization.

The program is written in MATLAB and C/C++, it requires MATLAB to run and saves the data in MATLAB (.mat) format. It also requires MATLAB's Image Processing toolbox.

Contents

• Buttons and controls - description of the program interface

• Output format - description of the data format for the data analysis

• Parameters - full list of parameters used by the program

• Adjusting parameters - important parameters and the process of their adjustment

• Protocols - several examples of the program use for typical tasks

• Typical problems - a few common problems