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Tracking cells or particles with lineage

Introduction

This guide explains you how to track cells or particles with lineage using the pipeline with the Blob Finder and Tracking operation. The purpose of the pipeline is to track objects, detected using the Blob Finder operation, gathering its motion features (direction, speed, linearity, and etc.) . Tracks division or fusion can be detected (lineage). It can be applied to cells, nuclei, or any detected structures.

Workflow

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

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

Opening the demo dataset

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

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.

Blob Finder

Automatic small objects detection algorithm. It uses a local threshold method.

Blob Finder parameters

Parameter	Description
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.

Blob Finder results

If you have set the parameters correctly, the preview (see Previewing the results) should look like this:

Store Objects

Store the detected segments (tag) in the active dataset.

Viewing the results

If not already visible, open the Objects dialog. In Shortcut Toolbar, click Objects table .
Measurements are now visible in the objects table.
To add or remove table columns, click Feature Columns...
For more information, refer to the Online Help (F1).

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.

Previewing the results

For all operations the preview is available in 2D, for some also in 3D.

Switch from 2D Viewer to 4D Viewer in the Viewer Type Switch.
To preview the operation results, click Preview in the Operation toolbar.

Use the Navigator panel in the Panel Sidebar to select the preview z plane and/or time points.

Adjusting the operations

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

You have opened the pipeline.

Go to the operation you want to change.
Set the appropriate parameters as desired.
Execute the pipeline (see Executing the pipeline).

Adding or removing operations

You can add or remove operations from the sample pipeline.

Click + Add operation...
The operation list is grouped in four groups by their typology.
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.
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.
To remove an operation, click Close at the Operation toolbar.