ZEISS Knowledge Base

Introduction

The guide explains you how to trace dendritic spines using the Spine Tracer operation included in the Tracing module. The operation provides 3 methods (AI-assisted, Use Segments and Use Probability Map) to detect and connect dendritic spines to an already existing trace. This guide focuses on the AI-assisted method.

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 demo dataset

To download the demo dataset, click https://demodata.arivis.com/data/arivisPro-DemoData-SamplePipelines-SpineTracer.zip (1).
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.

(1) Fernholz, Martin H. P. and Guggiana Nilo, Drago A. and Bonhoeffer, Tobias and Kist, Andreas M. "DeepD3, an open framework for automated quantification of dendritic spines", PLOS Computational Biology, 2024

Opening 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.

Activating the Sample Pipeline

In the Shortcut Toolbar, click Analysis Panel .
In the Sample Pipelines list, double-click the Detect Spines with AI assisted Method pipeline.
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.

The following operations are part of the pipeline.

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

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.

Neurite Tracer

Automatic tubular-like structures detection based on the threshold-based reconstruction algorithm.

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 color the results more meaningfully, click Set Object Style.
Click Apply to: Traces.
To select the trace color options, select one item from the Color by list.
To set further style settings, set the parameters in the Visualization section.