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. 


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:

  • thresFactorM (correction to the automatically detected background)

  • threshminlevel (fraction of pixels discarder in automatic background detection)

2. Edge/valley detection:

  • edgemode ─ "none" (or 0) - no edge detection, "log" (or 1) - Laplacian of Gaussian (LoG), "valley" (or 2) - Valley detection, "logvalley" (or 3) - both;

  • edgeSigmaL (parameter for LoG algorithm)

  • edgeSigmaV (parameter for Valley detection)

  • valleythresh1 (parameter for Valley detection)

  • valleythresh2 (parameter for Valley detection)

  • thresFactorM (thresholding parameter)

  • edgedetection, edgeSigma, logmode ─ obsolete parameters.

3. Splitting regions:

  • splitregions (parameter that determines whether a large region needs to be split)

  • areaMin (smallerst area of a region in sq. pixels, all smaller regions are discarder)

  • areaMax (largest area of the region in sq. pixels, all larger regions are split if splitregions is selected or discarder otherwise)

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.


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:

  • Next step - proceed one step and display the new outline

  • +100 steps - perform 99 steps silently and display the outline of the 100's one

  • Skip cell - finish the alignment of this cell silently

  • Continue - finish the alignment of this cell displaying every step without the need to press any button again

  • Debug - stop microbeTracker in debug mode (for example, to see the actual values of the forces)

  • Stop - terminate the process and exit MicrobeTracker (equivalent to Ctrl+C keyboard combination)

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.