This guide explains you how to detect neurons using the pipeline with the Neuron Tracer operation. The cell body is also detected, and it is used to start the tracing process. The operation offers algorithms to automatically segment neurons structures based on signal backbone seeds (local maxima) detection and their linking in a logical tree-like architecture. From the segments, several features are afterward measured.
Detecting neurons
Introduction
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-TraceCB.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.
Activating the Sample Pipeline
- In the Shortcut Toolbar, click Analysis Panel
.
- In the Sample Pipelines list, double-click the Detect Neurons 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.
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.
Input ROI parameters
|
Parameter |
Description |
|
|---|---|---|
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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. |
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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 |
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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. |
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.
Operation status
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...
- 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.
For some visualization examples, see Visualization Examples. - To set further style settings, set the parameters in the Visualization section.
For some visualization examples, see Visualization Examples.
Refer to the Help (F1) for more Information.
Visualization Examples
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Color by structure - Cone |
Color by structure - Approximation |
|
Color by depth - Approximation |
Color by depth - Skeleton |
|
Color by depth - Cone |
Editing the traces
The tubular structures segmented (traces) by the operation can be edited. Branches, terminal points, branches points, and other trace components are accessible for modification, optimizations, and improvements.
- In the Shortcut toolbar, click Trace Tool
.
- An Option Bar below the Shortcut Toolbar is displayed. Here you can find various tools with which you can draw or edit traces.
- Most of these tools can be activated using simple shortcuts to facilitate the workflow.
Refer to the Help (F1) for more details.