Abstract: A method for automatically adjusting gates to cytometry data of a target sample is provided. The method includes receiving training cytometry data corresponding to a plurality of training samples; generating an image of the target sample, generating images of the plurality of training samples; selecting a training sample from the plurality of training samples based on a similarity between the image of the selected training sample and the image of the target sample; calculating a transformation required to morph between the image of the selected training sample and the image of the target sample; and generating a target sample gate by applying the calculated transformation to the training gate associated with the selected training sample. A corresponding system and computer-readable medium are also provided.