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Tracking cells or particles

Demo dataset

The data set is a multi-dimensional, discrete representation of your real sample volume. It can be structured as a z-series of planes (optical slices) of multiple channels (dyes) in a temporal sequence of time points located at multiple spatial positions. Usually, the dataset shows a single experimental situation. A complete experiment can be composed by several datasets. The datasets are available as graphic files saved in plenty of file formats (standard formats as well as proprietary formats).

The link for the specific demo dataset for this guide is displayed below. All datasets are listed here: https://demodata.arivis.com

Downloading the demo dataset

  1. To download the demo dataset, click http://demodata.arivis.com/data/arivisVision4D-DemoData-SamplePipelines-3D_Tracking.zip.
  2. The download is starting automatically.
  3. Create a new folder on your local disk. Move the *.zip file from the download folder inside it.
  4. Unzip the folder.

Opening the demo dataset

  1. Click File > Open...
  2. Select the *.sis file from the Windows Explorer.
  3. The demo dataset is displayed in the viewer. The dataset is visualized according to the current rendering setting parameters.

Activating the Sample Pipeline

  1. In the Shortcut Toolbar, click Analysis Panel .
  2. In the Sample Pipelines list, double-click the Track Cells or Particles Pipeline.
  3. If you have activated a pipeline, it will be replaced by the new one.

You can open the appropriate How to guide. By hovering over a pipeline, this button is displayed. When clicking on it, the option Open How to appears.

Pipeline operations layout

The following operations are part of the pipeline.

Input ROI

This operation allows to select the region of interest (ROI). ROI defines the dataset subarea that will be processed and analyzed by the pipeline.

Input ROI parameters

Parameter

Description

ROI

Sets the processing and analysis target space.

–

Current View

The selected Z plane and the viewer area are processed.

–

Current Plane

The selected Z plane is processed (XY).

–

Current Time Point

The selected time point is processed (XYZ).

–

Current Image Set

The complete dataset (XYZ and time) is processed.

–

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.

Additional Parameters

Additional settings for Input ROI expand, when you click in the operation.

Parameter

Description

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.

Tracking

Track objects overt time according to the motion algorithm selected.

Tracking parameters

Parameter

Description

Input

Sets the objects to be tracked.

Motion type

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

–

Brownian Motion (Centroid)

Segments move more or less randomly in any direction.

–

Linear Regression (Centroid)

Segments move in a somewhat straight direction.

–

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.

–

Fusions

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

–

Divisions

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

–

Limit fusions

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

–

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.

Additional Parameters

Additional settings for Tracking expand when you click in the operation.

Parameter

Description

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.

Executing the pipeline

You can execute the pipeline step by step or in a single run. To do this, use the executing buttons in the Pipeline toolbar.

Executing Buttons in the Pipeline toolbar
Executing Buttons in the Pipeline toolbar

Executing step by step

You can execute the pipeline step by step (back and forth). This method allows to run and undo a single operation. You can either use the executing buttons in the Pipeline toolbar or in the Operation toolbar to go through the operation list.

  1. To run the single operation, click .
  2. To undo the single operation, click .
    Note: Undo the last operation executed if you need to change the operation settings.

Modifying the current pipeline

You can modify the pipeline to adapt to another datasets. Therefore, all the pipeline parameters should be set according to the new dataset features.

Adjusting the operations

The parameters of each operation are described here: Pipeline operations layout

  1. You have opened the pipeline.
  1. Go to the operation you want to change.
  2. Set the appropriate parameters as desired.
  3. Execute the pipeline (see Executing the pipeline).

Adding or removing operations

You can add or remove operations from the sample pipeline.

  1. Click + Add operation...
  2. The operation list is grouped in four groups by their typology.
  3. To add the operation to the current pipeline, double-click it. Alternatively, drag & drop the operation to the current Pipeline.
    Note:     The operation cannot be added during the Pipeline execution.
  4. The operation will be inserted at the end of the group of operations to which it belongs.
    Voxel operations are positioned before the segment generation. Store operations are always put at the end of the Pipeline.
  5. To remove an operation, click Close at the Operation toolbar.

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