Segementation

In the segmentation step, the pipeline performs instance segmentation on the image to generate a masks array of the same dimension as the input. The masks array is essentially the assignment of each pixel to a certain cell in the image. Hudson performs segmentation based on both cell and nucleic markers. Each cell is indexed as a label starting from 1 to the n’th cell that is segmented.Below are images of sample segmentation by this step with the original image (left) and masks outlining the different lables in the image (right).

The masks array is then saved for the next step of the pipeline