Active mask segmentation of fluorescence microscope images

Gowri Srinivasa, Matthew C. Fickus, Yusong Guo, Adam D. Linstedt, Jelena Kovačević

Research output: Contribution to journalArticlepeer-review


We propose a new active mask algorithm for the segmentation of fluorescence microscope images of punctate patterns. It combines the (a) flexibility offered by active-contour methods, (b) speed offered by multiresolution methods, (c) smoothing offered by multiscale methods, and (d) statistical modeling offered by region-growing methods into a fast and accurate segmentation tool. The framework moves from the idea of the "contour" to that of "inside and outside," or masks, allowing for easy multidimensional segmentation. It adapts to the topology of the image through the use of multiple masks. The algorithm is almost invariant under initialization, allowing for random initialization, and uses a few easily tunable parameters. Experiments show that the active mask algorithm matches the ground truth well and outperforms the algorithm widely used in fluorescence microscopy, seeded watershed, both qualitatively, as well as quantitatively.

Original languageEnglish (US)
Pages (from-to)1817-1829
Number of pages13
JournalIEEE Transactions on Image Processing
Issue number8
StatePublished - 2009


  • Active contours
  • Active masks
  • Cellular automata
  • Fluorescence microscope
  • Multiresolution
  • Multiscale
  • Segmentation

ASJC Scopus subject areas

  • Software
  • Computer Graphics and Computer-Aided Design


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