MotilityJ: An open-source tool for the classification and segmentation of bacteria on motility images.BACKGROUND AND OBJECTIVES
 Finally, we facilitate the dissemination of our pipeline with the development of MotilityJ, an open-source and user-friendly application for measuring bacteria spread on motility images.



MotilityJ
MotilityJ: An open-source tool for the classification and segmentation of bacteria on motility images.BACKGROUND AND OBJECTIVES

open-source tool
Such a pipeline consists of a classification model to determine whether the bacteria has spread to cover completely the Petri dish, and a segmentation model to determine the spread of those bacteria that do not fully cover the Petri dishes.  The classification model of our pipeline achieved a F1-score of 99.85%, and the segmentation model achieved a Dice coefficient of 95.66%. 
classification model
Such a pipeline consists of a classification model to determine whether the bacteria has spread to cover completely the Petri dish, and a segmentation model to determine the spread of those bacteria that do not fully cover the Petri dishes.  The classification model of our pipeline achieved a F1-score of 99.85%, and the segmentation model achieved a Dice coefficient of 95.66%.  In addition, the segmentation model produces results that are indistinguishable, and in many cases preferred, from those produced manually by experts. 
segmentation model
In this work, we address the problem of measuring bacteria spread on motility images by creating an automatic pipeline based on deep learning models.  In order to annotate enough images to train our deep learning models, a semi-automatic annotation procedure is presented.



deep learning models