Pipeline operations layout

ROI

Sets the processing and analysis target space.

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Current View

The selected Z plane and the viewer area are processed.

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Current Plane

The selected Z plane is processed (XY).

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Current Time Point

The selected time point is processed (XYZ).

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Current Image Set

The complete dataset (XYZ and time) is processed.

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Custom

Allows to mix the previous methods.
Note: Use the Custom option during the pipeline setting and testing. Set a sub volume (XY, Planes, Time Points, channels) of your dataset on which perform the trial. This will speed up the setting process.

Channels

Sets the processing and analysis target channels. Selecting a single channel, all the operations in the pipeline will be forced to use it.

Scaling

Sets the scaling of the dataset, which reduces it size. The measurements will not be modified by the scaling factor

Crop input data

Sets the limitation of the data used for the calculation to only the cropped selection defined above. If this option is not selected, the entire image set is used for the calculation.

Bounds

Sets the analysis area edges. The whole XY bounds, the viewing area or a custom space can be applied.

Planes

Sets the analysis planes range. A single plane, a range of planes or the whole stack can be selected.

Time Points

Sets the analysis time points range. A single time pint, a range of time points or the whole movie can be selected.

Channel

Sets the analysis target channel.

Diameter

Sets the reference objects diameter (max).
Note: Object diameter feature can be measured directly from the dataset with the Measurements tool.

Probability
threshold

Sets the probability threshold coefficient.
Note: You can use the Picker tool to pick a probability from the preview layer directly.

Split sensitivity

Sets the sensitivity used to split touching objects.

Decreasing the Split sensitivity will fuse more objects
.
Increasing the Split sensitivity will split more objects.

Note: You can use the Calculator tool, to compute the split sensitivity.

Input

Sets the objects to be tracked.

Motion type

Sets the type of motion that the segments perform. Three motion type algorithms are available.

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Brownian Motion (Centroid)

Segments move more or less randomly in any direction.

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Linear Regression (Centroid)

Segments move in a somewhat straight direction.

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Conal Angle (Centroid)

Segments move in a more restricted straight direction.

Max. distance

Sets the maximum distance that a segment can travel between time points.

Compute Max. distance

Sets whether the distance is computed automatically.

Track

Sets the track options. The parameter determines whether the segments should fuse or divide.

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Fusions

Enables the tracking of two or more segments fusing into a single segment over time.

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Divisions

Enables the tracking of one segment dividing into a two or more segments over time.

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Limit fusions

This parameter only appears when Fusions is activated. Restricts the number of segments that can fuse into a single segment simultaneously.

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Limit divisions

This parameter only appears when Divisions is activated. Restricts the number of segments into which a single segment can divide simultaneously.

Max. time gap

Sets the number of time points for calculating the average direction of a segment.

Continue tracks

Sets if the tracking of a given set of start objects. These objects can be segments, markers, or even tracks.

Centroid

Sets the method for calculating a segment's center. The methods Center of Bounding Box, Center of Geometry and Center of Mass (Intensity) (for each available channel) are available.

Weighting

Sets the features that should be considered during the tracking.