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Tips and Tricks to set parameters

Setting the parameters#

They are several tricks that can be used to increase tracking accuracy and select the optimal parameters.

Detection#

The detection parameters reject objects that are smaller or bigger than a specific size. To increase the tracking accuracy, we want to reject noise and artifacts and reject blobs constitute of more of one object. If all the objects are of similar size, these two parameters can be selected easily in four steps:

  • Select an image where two objects are in contact forming a single blob.
  • Select the Maximal Size parameter just at the limit to reject this blob.
  • Select the Maximal Size parameter just at the limit to detect the movie's smaller object.
  • Fine tune these parameters to account for size variability across the movie.

Tracking#

Tracking parameters are mostly found by trials and errors. However, some rules of thumbs can be applied.

Spot to track has to be set to Body for quasi-symmetric objects and low-resolution objects. For deformable objects with enough resolution, select Head or Tail according to the part that predicts best the object's traveling direction.

Parameters file#

For each tracking analysis, FastTrack will save the parameters used in cfg.toml that can be reloaded in the software or in fasttrack_cli. Before FastTrack version 5.2.1, the software used to saved the parameters in parameter.param, these files can be converted as following (left: old file, right: new file):

title = "FastTrack cfg""
[parameters]
Light background = 0 lightBack = 0
Maximal size = 170 maxArea = 170
Maximal occlusion = 200 maxDist = 200
Maximal time = 100 maxTime = 100
Background method = 1 methBack = 1
Minimal size = 50 minArea = 50
Morphological operation = 8 morph = 8
Kernel type = 2 morphSize = 2
Kernel size = 0 morphType = 0
Number of images background = 20 nBack = 20
Maximal angle = 90 normAngle = 90
Binary threshold = 60 normArea = 0
Normalization area = 0 normDist = 100
Maximal length = 100 normPerim = 0
Normalization perimeter = 0 reg = 0
Registration = 0 regBack = 0
Background registration method = 0 spot = 0
Spot to track = 0 thresh = 60
ROI bottom x = 0 xBottom = 0
ROI top x = 0 xTop = 0
ROI bottom y = 0 yBottom = 0
ROI top y = 0 yTop = 0