The pipeline have to be created according to the user analysis requirements as well as the sample typology. The sample labeling, the imaging technique (Fluorescence, EM, Tomography, bright-field ...) and the image characteristics are important to drive the pipeline setup. The knowledge of the biological structures under evaluation, it’s behavior and the expected features' trend are also important as well. All the above information should be used to build a target driven pipeline. The achieve the application note goals, only a couple of operators are mandatory. As described here below.

The Operators are grouped in several categories. Each category includes the functions that perform specific tasks, ordered by their usage. Here below a short summary.

Purpose

Application

Voxels Operator

The group includes the operators that interact directly with the voxels. Typically, spatial filters, Intensity normalization, intensity range equalization and so on.

Sample Noise removal, background subtraction, Intensity disomogenity correction, details enhancement, edges detection (e.g. membrane), morphological math.

Segmenter Generation

The group includes the threshold operators used to detect and create the segments. Automatic and manual method, machine learning approach, watershed and proprietary algorithms are available.

Structures identification. Nuclei, Neurons, small spots (Blob Finder), Cells, Vessels, Filaments (Watershed, Region Growing) or microstructures (Machine learning) can be detected using the appropriate method or a combination of them.

Segmenter Operators

The group includes the operators that interact directly with the segments. Feature filtering, morphology, Compartmentalization, distance measurements and more can be applied.

Objects colocalization, object classification by features, objects merging or splitting, objects grouping, objects parent/child relationship and even more.
  1. Change the Input ROI operator parameters.
  2. 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.
  3. Expand the Input ROI dialog.


    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 TP, a range of TPs or the whole movie can be selected.
  4. Channels: Sets the processing and analysis target channels. Selecting a single channel, all the operators in the pipeline will be forced to use it.
    Scaling: It scale the dataset reducing the size.​ The measurements will not be modified by the scaling factor.​
  5. Set the Import Document Objects operator and select the TAG filter.
  6. Click on the Manual TAG.​
  7. Use the right arrow button to move the TAG on the right table​.

  8. Add or remove optional operators inside the pipeline.

    The Analysis Pipeline panel consists of two main areas. The Pipeline area and the analysis operations list area.​

    The Operators can be added to Pipeline in two ways:
  9. Double click on the Operator you wish to add to the current Pipeline. The Operator will be inserted at the end of the group of operations to which it belongs. Voxel Operations are positioned before the Segment generation meanwhile Store operations are put always at the end of the Pipeline.
  10. Drag and drop the Operator you wish to add to the current Pipeline. The Operator will be automatically inserted in any place within the group of operations to which it belongs. The Operator cannot be added during the Pipeline execution.
  11. To remove an Operator from the Pipeline, press the X button located in the right side of the operator title bar.

Refer to the arivis Pro Help for more details.