This guide explains you how to detect cells or particles using the pipeline with the Blob Finder and Feature Filter operations. The purpose of the pipeline is to detect objects having a quite limited, well defined, structure. The pipeline can be applied to cells, nuclei, or any kind of small particles.
Detecting cells or particles
Introduction
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-Particles.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.
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 |
|
|---|---|---|
|
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. |
|
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. |
Object Feature Filter
Allows the segments filtering based on multiple parameters selection.
Object Feature Filter parameters
|
Parameter |
Description |
|
|---|---|---|
|
Input |
Sets the filter input. If more than one segment operation is present in your pipeline, the correct input source must be set. |
|
|
Is of type |
Sets the type of filter which filters the objects based on the selected type. By default, it is set on Any for all object types. The list of available features is updated accordingly. |
|
|
Filter selection |
Sets the function for the segmentation is performed. |
|
|
Criterion Settings |
These parameters depend on the selection of the filter. |
|
|
+ Add Filter |
Allows to add a Simple, Ratio or Tag filter criterions. |
|
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...
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.
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.