Detecting small structures (Watershed)

Introduction

This guide explains you how to detect small structures using watershed using the pipeline with the Normalization and Watershed operation. The purpose of the pipeline is to detect objects having almost any shape. The pipeline can be applied to cells, nuclei, or any kind of small 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

To download the demo dataset, click http://demodata.arivis.com/data/arivisVision4D-DemoData-SamplePipelines-Watershed.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.

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 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.

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

Operation status

Executing buttons in the Operation toolbar after executing

When the operation is running, this icon is shown.

When the operation is completed, this icon is shown.

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).