2.2 Image Segmentation

1. Adjust Mask Parameters

2. Click Compute Mask

Make sure every cell is outlined and there are no opening of the mask inside cells (if this happens in a few cells it’s not a problem, however those cells need to be discarded in the last step)

Mask Algorithm:

• Isodata - one threshold value for whole image
• Local Average - local threshold values

  • Local Average blocksize: size in pxs of the local area to calculate thresholds

  • Local Average Offset: value to be subtracted from automatic calculated thresholds

• Fill holes: fills openings inside the mask
• Mask closing: removes sharp edges of mask (adjust value by increments of 1)
• Mask dilation: expands mask to the background (adjust value by increments of 1)