Step 9: Export Results

Step 9: Export Results#

Once satisfied with your selection, export the results.

Export to XML#

Click “Export as XML” to save your selection in LMD-compatible format:

  • You’ll be prompted for a base filename

  • CellPick creates multiple output files: - <name>.xml: Shape coordinates in the original format, compatible with LMD systems - <name>.csv: Cell IDs with spatial scores (if landmarks were used) - <name>_landmarks.xml: Landmark polygons (if landmarks were used) - <name>_AR.xml: Active region polygons

Note

If you loaded a downscaled image, CellPick automatically scales coordinates back to full resolution on export.

Export to SpatialData#

Click “Export to SpatialData” to save your selection to a .zarr store:

  • Creates a new SpatialData object with: - Selected shapes as polygon geometries - Associated table with selection metadata

  • Compatible with the SpatialData ecosystem for downstream analysis

Save Screenshot#

To save a screenshot of the current view:

  • Use the menu: File → Save Screenshot…

  • Or use the keyboard shortcut: ⌘+Shift+S (Mac) / Ctrl+Shift+S (Windows/Linux)

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