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Detecting dendritic spines (Segments)

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 segments method.

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 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 Use Segments 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.

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 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.

Refer to the Help (F1) for more Information.

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.