Step 7: Landmark Selection (Optional)

Step 7: Landmark Selection (Optional)#

Landmarks define a spatial gradient for scoring cells. Adding two landmarks allows CellPick to assign a score to each cell based on its position between the landmarks.

Adding Landmarks#

  1. Click “Add Landmark” to enter selection mode

  2. Right-click on the image to add points defining the landmark boundary

  3. Click “Confirm” when done (minimum 3 points required)

  4. Repeat for the second landmark

Landmark Selection

Gradient Scoring#

After adding both landmarks:

  • Each cell is automatically assigned a score based on its distance to both landmarks

  • Cells closer to landmark 1 receive a lower score (rendered in red)

  • Cells closer to landmark 2 receive a higher score (rendered in green)

  • Cells equidistant from both landmarks have a score near 0.5

Gradient assignment

Managing Landmarks#

  • Delete Last Point: While adding, click “Undo” to remove the last point

  • Delete Landmark: Click “Delete Landmark”, then right-click on a landmark to remove it

  • Load from File: Click “Load from File” to import landmarks from a previously saved XML file

Note

If both labels and landmarks are loaded, you can toggle between label colors and gradient colors using View → Show Gradient or the keyboard shortcut ⌘+Shift+G (Mac) / Ctrl+Shift+G (Windows/Linux).

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