ZEISS Knowledge Base

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-Membrane.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.

The following operations are part of the pipeline.

Membrane Detection

The filter is used to enhance the membrane edges.

The Membrane Detection operation is a complex algorithm. Its execution can take long time.

Membrane Detection parameters

Parameter		Description
Channels		Sets the processing and analysis target channels.
Membrane width		Sets the width of the membranes to be enhanced. You can enter the membrane width as a world space distance (e.g., µm) or in pixels. Note: You can measure the width directly from the dataset with the Measurement tool.
Max. gap size		Sets the size between gaps to be closed. You can enter the max gap size as a world space distance (e.g., µm) or in pixels Note: You can measure the gap size directly from the dataset with the Measurement tool.

Detects the cell body starting from the membrane marker.

Parameter		Description
Channels		Sets the processing and analysis target channels.
Min intensity (membrane)		Sets an approximation of a membrane with the lowest intensity. This value is used for the initial thresholding of the image to extract the membrane and thus separate it from the background. This is a very important and guiding value, therefore it needs to be selected carefully.
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.
Membrane Maximum		Sets the membrane maximum size. Drop down the list to select the feature
–	Max. diameter	Sets the value as the maximum diameter. Note: You can measure the membrane maximum diameter directly from the dataset with the Measurement tool.
–	Max. area	Sets the value as the maximum area. Note: You can measure the membrane maximum diameter directly from the dataset with the Measurement tool.
–	Max. volume	Sets the value as the maximum volume. Note: You can measure the membrane maximum diameter directly from the dataset with the Measurement tool.

Membrane-based Segmenter 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.

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.