Phase contrast 
Thresholding only

Valley,
σ = 0.5, t1
= 0, t2
= 0.06


Valley,
σ = 1, t1
= 0, t2
= 1.8

Valley,
σ = 0,
t1
= 0, t2
= 1.8

Valley,
σ = 0.5, t1
= 0, t2
= 30

Valley,
σ = 0.5, t1
= 0, t2
= 0.6

Valley,
σ = 0.5, t1
= 2.4, t2
= 1.8

Valley,
σ = 0.5, t1
= 0, t2
= 1.8

The effect of parameters on
the valley detection algorithm and its comparison with LoG 
Edge and valley detection is used to supplement thresholding in
initial segmentation of the cells. MicrobeTracker uses two algorithms for this
purpose:
While LoG with zero threshold has empirically proven to be the
best out of the standard edge detection algorithms, Valley detection was
developed for MicrobeTracker, and though it depends on a large number of
parameters, in some cases it generates superior results. The algorithm which
MicrobeTracker uses
is defined by the following parameter:

edgemode
─ "none" (or 0)  no edge detection, "log" (or 1)  Laplacian of Gaussian
(LoG), "valley" (or 2)  Valley detection, "logvalley" (or 3)  both,
"clogvalley" (or 4)  crossdetection mode without direct LoG or Valley.
Laplacian of
Gaussian
This algorithm applies a Gaussian filter (which smoothes the image), followed by
a Laplacian filter (resulting in a combined "mexican hat" filter). The points of
zero crossing of the resulting image are considered to be parts of the 'edge'.
The algorithm (as implemented here) depends on two parameters:
Valley
detection
This
algorithm applies a Gaussian filter (which smoothes the image), followed by
finding local minima with the second derivative above a threshold. The function
uses two thresholds: a strong one, always indicating a valley pixel, and a weak one, only
indicating a valley pixel if it is adjacent to a pixel identified using the
strong threshold. The parameters:

edgeSigmaV
─ width of the smoothing Gaussian. Must be zero or above. Default: 0.5.

valleythresh1
─ weak threshold. Must be above the strong threshold. Default: 0.

valleythresh2
─ strong threshold. Default: 1.
Crossdetection mode
There is also a crossdetection mode, combining the two algorithms above. The
mode is activated in the "logvalley" or "clogvalley" modes. In the "logvalley"
mode the edges detected by all three algorithms are combined, while the
"clogvalley" mode only results in the crossdetected edge. This mode depends on
one additional parameter:
