Stopy: Manual

StopyApp is a semi-automatic tool for the analysis of Solid State Nuclear Track Detectors. It is designed to simplify the analysis process as much as possible.

List of Terms

• Project: Contains several Samples, typically obtained from a single measurement.
• Sample: Represents a single detector. The main parameters are the input image and the directory for results.
• Track: A single detection represented by an ellipse.
• Candidate: One or more tracks where ellipse extraction was unsuccessful; manual intervention is required.

Basic Usage

• When the application starts, the Project View opens by default.
• The user can add Samples to the project or scan a directory to automatically detect all available samples.
• Next, an automatic analysis is run. The duration of this process depends on the number and size of the Samples, as well as the number of tracks per Sample. Processing a single Sample may take several minutes.
• Once the automatic analysis is complete, the user can review the samples individually to mark any tracks that the automatic algorithm may have missed.
• The Sample View displays all detected tracks, along with regions where the algorithm identified candidate areas but could not extract tracks.
• The results for each Sample are stored in a directory containing:
  • tracks.json: internal format used to store track information.
  • tracks.nap: NAP file containing tracks for compatibility purposes.
  • candidates.json: internal file that stores information about candidate regions.

Project View

The Project View displays an individual project and provides tools for working with it.

Toolbar

• New Project: Create a new project workspace.
• Load Project: Open an existing project from storage.
• Save Project: Save the current project.
• Save Project As: Save the current project under a new filename or location.
• Add Sample: Manually add a sample, which will insert a new entry in the Sample List.
• Scan Directory: Search a specified directory for samples. The operation prompts for the directory to scan and a target output directory. The program searches for sample directories following the pattern (name)/001/Img in the file path.
• Update Statistics: Update and display the current counts of tracks and candidates.
• Run All: Queue all current samples for processing and initiate the processing of the first sample.

Sample table

• Name: Name of the sample.
• Image: Path to the image file, or to te directory containing all microscope images for the sample.
• Output: Output directory for this sample; analysis results are stored here.
• Tracks: Number of tracks detected in this sample.
• Candidates: Number of candidate objects detected in this sample.
• Actions:
  • Open: Open the sample in the Sample View.
  • Run: Add this sample to the processing queue. If the queue is empty, processing will begin immediately.
  • Delete: Remove this sample from the project. This action will not delete the results; delete results manually if required.

Output Area

The output area displays the output generated by the stopy library.

Sample View

Tracks Toolbar

The tracks toolbar displays the number of tracks and provides detailed information about the currently selected track. It includes a button to show the list of tracks and another button to toggle the visibility of tracks in the image.

Candidates Toolbar

The Candidates toolbar allows the user to review all possible detections that the automatic algorithm was unable to extract. It displays information about the currently selected candidate and the total number of candidates. The user can navigate between candidates by pressing the Prev and Next buttons. If there are no remaining unresolved tracks for the candidate, the Check and Next button will mark the candidate as resolved and proceed to the next one.

Manipulating tracks

There are several tools available for track manipulation:

• Selection tool: When the selection tool is active, the user can click on a track (ellipse) to select it. Pressing the Delete key will remove the selected track.

• Manual ellipse drawing: The user can manually place points to define the shape of an ellipse.

• Semi-automatic method: This tool allows for partial automation in the process of track construction.

Add ellipse by draing points on a perimeter

When this tool is activated, the user can add a track (ellipse) by drawing points with the Left-Mouse-Button along the perimeter of the intended ellipse. Once at least five points are placed, an ellipse is fitted to these points. As more points are added, the ellipse is continuously updated to best match all selected points, enabling precise refinement of its shape. When the user is satisfied with the fitted ellipse, pressing the Right-Mouse-Button adds the track to the list of tracks.

This manual method provides the highest accuracy for adding tracks; however, for datasets containing many tracks, the semi-automatic approach is considerably more efficient.

Sami automatic method

When this tool is activated, use it to draw circles by pressing the Left-Mouse-Button at the desired center point and dragging outward to set the radius; release the Left-Mouse-Button to complete the circle. Multiple circles can be drawn in this manner. By clicking the Right-Mouse-Button, the algorithm attempts to optimally fit ellipses to the drawn circles, thereby achieving better coverage of the tracks.

This method can provide significant speed improvements over manual tracing. However, it may be unreliable when dealing with more complex groups of tracks.