This guide explains you how to detect big structures manual using the pipeline with the Intensity Threshold Segmenter operation. The purpose of the pipeline is to detect objects having a random shape and not well-defined borders. It can be applied to any cellular compartments or biological structures.
Detecting big structures manually
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 https://demodata.arivis.com/data/arivisPro-DemoData-SamplePipelines-3DStack.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 Big Structures Manual 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.
Denoising
Set of operations performing noise reduction. Choose the more suitable method based on your sample and define the diameter.
Intensity Threshold Segmenter
Allows the segments detection using one of the available automatic threshold methods.
Intensity Threshold Segmenter parameters
By default, the Method: Range is selected. Depending on the selection, different parameters are available.
|
Parameter |
Description |
|
|---|---|---|
|
Channel |
Sets the processing and analysis target channel. |
|
|
Method |
Sets the threshold algorithm. By default, Auto is selected. |
|
|
– |
Simple |
This method uses a single threshold and segments everything below or above it. |
|
– |
Range |
This method uses two Thresholds to define the range of intensities to segment. Everything outside of this range is neglected. |
|
– |
Percentile |
This method uses a single threshold and segments all intensities below or above it. The threshold is given as a percentile and is based on the data. |
|
– |
Percentile range |
This method uses two thresholds to define the range of intensities to segment. Everything outside of this range is neglected. The thresholds are given as percentiles and are based on the data. |
|
– |
Auto |
This method uses a single threshold and segments all intensities below or above it. The threshold is automatically calculated based on the data. |
|
– |
Adaptive mean |
This method uses local information around each pixel to set a threshold in relation to the local background. It is based on Niblack's thresholding method. |
|
– |
Mean |
This method uses local information around each pixel to set a threshold in relation to the local background. |
|
Threshold |
Sets the threshold values accordingly to the image dynamic range. |
|
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.
Executing in a single run
As alternative to executing step by step, execute the pipeline in a single run.
- To run the whole pipeline, click
.
- To stop the pipeline execution, click
.
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 show the results of each tag, click Single.
- For more information, refer to the Online Help (F1).
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.