SegRef3D

SegRef3D Tutorial (English)

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🕹️ Basic Controls

• 🔄 Switch images
  • Next image: PageDown, F, or J
  • Previous image: PageUp, R, or U
• 🔍 Zoom in/out
  • Zoom in: E, I, +, or =
  • Zoom out: Q, P, or -
  • You can also use Ctrl + scroll
• 🧭 Pan the image when zoomed
  • Move up: W, O, or ↑
  • Move down: S, L, or ↓
  • Move left: A, K, or ←
  • Move right: D, ;, or →
  • You can also use scroll, or Shift + scroll for horizontal panning
• ✏️ Drawing in Click mode
  • Confirm current drawing: G or H
  • Undo the last click point: T or Y
• ↩️ Undo / Redo
  • Undo drawing line: Undo Line
  • Redo drawing line: Redo Line
  • Undo mask edit: Undo Edit
  • Redo mask edit: Redo Edit
  • Shortcut: Ctrl + Z if implemented

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🔄 Basic Workflow

🤖 Automatic Segmentation

1. Click Load Images to import images.
2. Click Prepare Tracking to prepare the tracking process.
3. Use Set Box Prompt to define a rectangular region around the target.
4. Navigate to the start image for tracking, then click Set Tracking Start.
5. Navigate to the end image for tracking, then click Set Tracking End.
6. Click Run Tracking.
   This may take some time depending on the number of images and your computer environment.
7. Select the Target Object number, then click Add to Mask to register the mask.
8. Use the checkboxes at the bottom of the window to show or hide each object mask.

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✏️ Editing / Refinement

• Draw directly on the image using a mouse or stylus.
• Select the object number to edit using Target Object.
• To add the drawn region to the selected object, click Add to Mask.
• To remove the drawn region from the selected object, click Erase from Mask.
• Select the pen color using Pen Color.
• Select the drawing mode using Draw Mode.
• Drawing lines can be controlled using Undo Line, Redo Line, Clear Lines, and Clear All Lines.
• Mask editing operations can be undone or redone using Undo Edit and Redo Edit.

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🔁 Transfer Masks Between Objects

• Select the source object using Target Object.
• Specify the destination object number using Transfer To:.
• This can be used to transfer an existing mask from one object to another when needed.

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💾 Save Mask Data

• Click Save Masks to save the current mask data.

• To resume editing later, load the data in the following order:

  • Click Load Images to import the image sequence.
  • Click Load Masks to load the saved mask data.

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📏 Calibration

• Enter the actual length of the reference line in Line Length (mm).
• Enter the Z-direction interval between images in Z Interval (mm).
• Click Calibration Line and draw a reference line on the image.
• After calibration, the scale is applied to distance measurement and 3D export.

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📐 3D Export

• Set Smooth Level and Smooth Mode as needed.
• Click Export 3D to export 3D data.
• Use external software to view the exported 3D data.
  Examples: 3D Slicer, MeshLab

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📊 Volume Information

• Click Load VolInfo to load volume information.
• Click Show VolInfo to display volume information.
• Volume calculation reflects the calibration data and Z-direction interval.

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📏 Distance Measurement Between Two Points

• Click Measurement Line.
• Click two points on the image to draw a measurement line.
• If calibration has been completed, the actual distance is displayed in millimeters.
• The measurement result is temporarily displayed on the screen.
• Click Export Measurements to export the measurement results.

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🧩 Advanced Functions

The following functions are available from Extensions in the lower-left area of the window.

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🔁 Batch Tracking for Multiple Objects

1. Select the batch tracking function from Extensions.

2. For each object, specify the following:

   • Box Prompt
   • Tracking Start and End
   • Add Object Prompt
3. After all target objects have been specified, click Run Batch Tracking.

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🎚️ Threshold-Based Extraction

1. Select the threshold extraction function from Extensions.
2. Set Threshold min and max.
3. Click Extract by Threshold to extract regions within the specified threshold range.
4. Click Add to Mask to add the extracted region to the target object.
5. If preset options are available, you can select presets such as CT Soft Tissue.

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🖍️ RGB Color Extraction

1. Select the RGB color extraction function from Extensions.
2. Specify the R/G/B values and tolerance range using Target RGB and ±Tol.
3. Click Extract by RGB to extract regions close to the specified color.
4. Use Pick Color to click on the image and automatically retrieve RGB values.
5. Click Add to Mask to add the extracted region to the target object.

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🧹 Remove Small Mask Fragments

1. Select the small-fragment removal function from Extensions.
2. Specify the target object number using Delete Object.
3. Enter the area threshold in Threshold(px^2).
4. Click Remove Small Parts to remove small mask fragments below the specified area threshold.

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❌ Delete Segmentation Masks

1. Select the mask deletion function from Extensions.
2. Click Delete Object CurrentImg to delete the target object mask only from the currently displayed image.
3. Click Delete Object AllImg to delete the target object mask from all images.

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📝 Notes

• Reorder, Bring to Front, and Send to Back have been removed and are not used in ver.1.2.0.
• In ver.1.2.0, the internal image-processing workflow has been improved, and mask processing has been unified into a raster-based workflow.
• Functions that are not always visible in the main UI are generally available from Extensions.

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