Orientation Computation

The Orientation Computation feature in VASCilia calculates the orientation angles of labeled volumes in cochlear datasets. This tool is essential for analyzing the structural alignment and orientation of cellular components.

Key Features

1. Orientation Points Calculation:

   • Identifies the leftmost and rightmost points of each labeled region.

   • Supports two methods: - Height_only: Uses the height of the lowest points to compute orientation. - Height_Distance: Combines height and distance from the peak point for a more robust calculation.

2. Angle Calculation:

   • Computes the orientation angle between the identified points for each region.

   • Outputs angles in degrees.

3. Interactive Visualization:

   • Displays orientation lines, points, and angle annotations in the Napari viewer.

   • Updates lines and angles dynamically in response to user modifications.

4. CSV Export:

   • Saves the calculated angles and their associated labels to a CSV file in the orientation directory.

Usage Instructions

1. Choose Method:

   • Use the Compute Orientation widget to select a method: Height_only or Height_Distance.

2. Compute Orientation:

   • Click the Compute Orientation button to calculate the orientation points, lines, and angles.

3. Review Orientation:

   • Orientation lines, points, and angles are displayed in the viewer:

     • Orientation Lines: Yellow lines connecting the identified points.

     • Orientation Points: Magenta points marking key locations.

     • Angle Annotations: Lime green text displaying the angles.

4. Save Results:

   • Results are automatically saved to the orientation directory in the project folder:

     • angle_annotations.csv contains the computed angles and their corresponding labels.

Example Workflow

1. Open the Orientation Computation widget in the plugin interface.

2. Select the preferred computation method (Height_only or Height_Distance).

3. Click Compute Orientation to calculate and visualize the orientation.

4. Adjust visibility of layers in the viewer as needed.

5. Access saved angle data in the orientation directory for further analysis.

Practical Considerations

• The Height_only method is simpler and suitable for BASE and MIDDLE datasets.

• The Height_Distance method provides more accurate results for APEX datasets.

• Adjustments to orientation points and lines are dynamically reflected in the visualization.

Outputs

1. Visualization Layers:

   • Orientation Lines: Yellow lines connecting points of interest.

   • Orientation Points: Magenta points marking key regions.

   • Angle Annotations: Text annotations of calculated angles.

2. Saved Data:

   • angle_annotations.csv: Contains the label IDs and corresponding angles in degrees.

Extending the Functionality

To add or modify functionality, edit the following file:

• compute_orientation_action.py

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