Step 8: Shape Selection

Step 8: Shape Selection#

With active regions defined, you can now select cells using various algorithms.

Selection Methods#

CellPick offers four selection methods (available in the dropdown):

  1. Select k over union of regions: Uses the Gonzalez k-center algorithm to select k cells distributed across all active regions combined. This maximizes spatial coverage while ensuring selected cells are not contiguous.

  2. Random: Randomly selects k cells from all active regions.

  3. Select k per region: Selects k cells from each active region independently, using the k-center algorithm per region.

  4. Select k per label: (Requires loaded labels) Selects k cells from each cell type label. Only visible when labels are loaded.

Shape Selection

Automatic Selection#

  1. Enter the desired number of cells in the k spinner

  2. Select a method from the dropdown

  3. If using “Select k per label”, check/uncheck labels to include/exclude

  4. Click “Automatic Selection”

  5. Selected cells will be highlighted in the image

Per-label selection with label checkboxes
Multiple Active Regions with selected cells
Per-region selection across multiple active regions

Manual Editing#

After automatic selection, you can manually refine your selection:

  • Add Shapes: Click “Add”, then right-click on a cell to add it to the selection

  • Remove Shapes: Click “Delete”, then right-click on a selected cell to remove it

Warning

CellPick will warn you if selected shapes are contiguous (touching). For laser microdissection, non-contiguous cells are typically required.

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