The SegmentationMask is an integer array the same size as the x-y plane of the input ImageStack. The values of the SegmentationMask indicate which cell each pixel corresponds to. At the moment, only hard assignment is supported.


The SegmentationMask is currently implemented as a numpy.ndarray object. We are revisiting the optimal object for this information, and are aware of the pending need to use segmented instances of cells to label points in 3d, and also to support non-cell instances. The current implementation is expected to change.


numpy arrays can be saved in a variety of formats of which the most common is npy