paper information and status

G. Srinivasa, M. C. Fickus, Y. Guo, A. D. Linstedt and J. Kovačević. Active mask segmentation of fluorescence microscope images. IEEE Trans. Image Process., 18(8):1817-1829, Aug. 2009.

[ pdf | @ IEEE Xplore | bibtex]


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) blurring 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.


The zipped archive contains the images from five different stacks used as test data in this study.


Details about the preparation of data and imaging as well as the details for citing the images in your own work can be obtained from Linstedt Lab.



The zipped archive contains the readme file as well as the code to generate the results in the paper.



The zipped archive contains a help file and the ImageJ plugin.


This work is licensed under a Creative Commons GNU General Public License. To view a copy of this license, visit If you use this code or any part thereof in your research or publication, please also include a reference to this paper. Thank you!

other material

The zipped archive contains hand-segmented masks for the test images as well as valid cell masks for seeded watershed and active mask algorithms (with automatic and hand-drawn seeds) and all of the intermediate results together with their respective MATLAB scripts used to generate Table II.


list of tested configurations

MATLAB 7.0.1 on Windows XP Professional

(Note: Seeded watershed with perfect seeds does not work on this version)

MATLAB 2007a on Windows XP Professional


For more information or to report bugs contact jelenak at cmu dot edu.