Parameter testing mode

The panel shown above is located in the lover right corner of MicrobeTracker window. The mode is designed to display normally hidden intermediate images for the purposes of choosing the optimal parameters for a particular image. There are two parameter testing regimes: Segmentation and Alignment. Segmentation mode will preview the segmented image before the alignment started with the current parameter set (the only mode is algorithm 1 is selected), while Alignment mode will display the process of the active contour fitting to each cell. 

Segmentation

This mode previews the segmented image for the current frame before the contour alignment starts and opens a separate MATLAB figure with the result. If Selected area is chosen, it only processes this area (see the image to the right). If no area is selected, the whole image gets processed.

This regime consists of three steps, each of the affected only by a small number of parameters.

1. Thresholding:

2. Edge/valley detection:

3. Splitting regions:

In algorithm 1, every segment of the correct size range is outlined directly. In the rest of the algorithms, the segmentation is followed by contour creation and alignment.

Alignment

The Alignment button on the Parameter test mode panel lets the user to see the process of alignment dynamically. After activating the mode, click any processing button (such as All frames, This frame, Range, buttons for manual operations) to see the how alignment happens.  Note, MicrobeTracker still saves the data in memory and to the disk after each frame (if selected), so be careful to not erase your data!

This regime when activated is equivalent to fitDisplay and fitDisplay1 parameters present and set to 1. While fitDisplay allows the user to see the alignment process to the image, fitDisplay1 allows for seeing alignment to the roughly segmented region in algorithms 2 and 3 only (it will have no effect in algorithm 4). The alignment procedure is different depending on what cell outlining algorithm is used. For example, since there is no alignment in algorithm 1, these parameters and the Alignment button will have no effect.

Buttons of the alignment tool:

The color codes used to display the outline and forces for algorithm 4 are shown on the second figure. Algorithms 2 and 3 use only the image forces, the constrains are implemented in a different way and are not displayed.

 

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