Topology preserving STACS segmentation of protein subcellular location images

We present an algorithm for the segmentation of multicell fluorescence microscopy images. Such images abound and a segmentation algorithm robust to different experimental conditions as well as cell types is becoming a necessity. In cellular imaging, among the most often used segmentation algorithms is seeded watershed. One of its features is that it tends to oversegment, splitting the cells, as well as create segmented regions much larger than a true cell. This can be an advantage (the entire cell is within the region) as well as a disadvantage (a large amount of background noise is included). We present an algorithm which segments with tight contours by building upon an active contour algorithm - STACS, by Pluempitiwiriyawej et al. We adapt the algorithm to suit the needs of our data and use another technique, topology preservation by Han et al., to build our topology preserving STACS (TPSTACS). Our algorithm significantly outperforms the seeded watershed both visually as well as by standard measures of segmentation quality: recall/precision, area similarity and area overlap