Adjusting Parameters

This section describes how to select the parameter file and to adjust the most sensitive parameters for a particular experiment. For a detailed description of all parameters see the Parameters page. After you have adjusted the parameters and the result seems to be good, you should save the parameter set to use in the future with similar experiments. The set you used before can also be retrieved from a saved results (meshes) file (make sure in this case that you select .mat filter when loading the file). If saved in a separate file (.set), the parameters can be edited with any external text editor.

1. Algorithm

The typical choice is algorithm 4, sometimes 1, and more rarely 2, they are selected by setting algorithm=1, algorithm=2, etc. Try algorithm 4 first, unless it is clear a different one should be used. The algorithm 3 has practically no benefits over the other algorithms, and therefore has not been tested in the latest versions of the program. The choice of the algorithm will mostly depends on the type of the image and of the cells. See Cell outlining algorithms page for more details.

2. Default parameter sets

After you have decided what algorithm to use, load the corresponding predefined set. There are several general sets alg1.set, alg2.set, alg4.set tested for C. crescentus under the resolution ~ 0.06 µm/px. Some other sets were tested for other cell types, such as alg2ecoli.set and alg4ecoli.set for E. coli cells under the same resolution. For other cells just select one of the standard sets and modify some of the parameters if necessary.

3. Image segmentation

Image segmentation is performed in two steps: thresholding and edge detection:

4. Other shape-related parameters

5. Aligning the shape

6. Splitting and joining cells

 

See also: Parameters. Top pages: MicrobeTracker, MicrobeTracker Suite.