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Post-Processing SKeMa Output

SKeMa produces a binary GeoTIFF where 1 = kelp and 0 = background. This guide covers converting that raster to polygons and optionally removing false positives caused by eelgrass beds.

Step 1: Vectorize the Raster

  1. Load the output .tif in ArcGIS Pro
  2. Open the Geoprocessing panel and run Raster to Polygon:
    • Input raster: your kelp output .tif
    • Field: Value
    • Uncheck Simplify polygons for maximum accuracy
  3. Delete polygons where gridcode = 0 (background class) from the attribute table
  1. Load the output .tif in QGIS
  2. From the menu, go to Raster → Conversion → Polygonize (Raster to Vector):
    • Input layer: your kelp output .tif
    • Name of the field to create: value
  3. Delete features where value = 0 (background class) using Select by Expression, then Delete Selected Features

Step 2: Remove Small Polygons

Isolated single-pixel predictions are almost always noise. Delete polygons with an area below your minimum mapping unit (a threshold of 100 m² works well for 10 m Sentinel-2 data).

Use Select by Attributes to select features where Shape_Area < 100, then delete them.

Use Select by Expression with $area < 100, then Delete Selected Features.

Step 3: Optional — Remove Eelgrass False Positives

Kelp predictions overlapping eelgrass (Zostera marina) beds are typically false positives. Eelgrass occupies similar shallow depths to kelp, and the model can confuse dense eelgrass patches when viewed from satellite.

The BC Marine Conservation Analysis (BCMCA) provides an eelgrass habitat polygon dataset for British Columbia. Download the eelgrass layer from DataBC (search "BCMCA eelgrass") and use it to erase overlapping kelp predictions.

  1. Load your kelp polygon layer and the BCMCA eelgrass polygon layer into the same map
  2. Open the Geoprocessing panel and run the Erase tool:
    • Input Features: your kelp polygons
    • Erase Features: BCMCA eelgrass polygons
    • Output Feature Class: kelp_no_eelgrass
  3. Inspect the output to confirm eelgrass areas have been removed
  1. Load your kelp polygon layer and the BCMCA eelgrass polygon layer
  2. Go to Vector → Geoprocessing Tools → Difference:
    • Input layer: your kelp polygons
    • Overlay layer: BCMCA eelgrass polygons
    • Difference: save as kelp_no_eelgrass.shp
  3. Inspect the output to confirm eelgrass areas have been removed

Step 4: Export

Export the final layer as a shapefile or GDB feature class with an appropriate name. That's it!