Abstract
In this paper we present a ImageJ plugin for easy development of image segmentation (clustering) pipelines. Main focus of our approach is to provide scientists working with various images (especially biological and medical ones) with a tool making development of segmentation pipelines fast and easy. We accomplish this by introducing an extra abstraction layer to the ImageJ image segmentation approach – the feature space projection – that enables us to work with complex image descriptors and manage, visualize and test them directly from the plugin. Furthermore we give three separate ways of expressing such projections – one based on Java language, one based on external scripting and one on our custom simple Micro Matrix Language. The plugin can also serve as a fast method of rapid prototyping of image filters while its full ImageJ macro support makes it really easy to include it in ones current image processing methods.
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References
Andlauer, T.F.M., Sigrist, S.J.: Quantitative analysis of Drosophila larval neuromuscular junction morphology. Cold Spring Harbor Protocols 2012(4), 490–493 (2012)
Carreras, I.A.: Advanced WEKA Segmentation (2011), http://fiji.sc/wiki/index.php/Advanced_Weka_Segmentation
Dello, S.A.W.G., Stoot, J.H.M.B., van Stiphout, R.S.A., Bloemen, J.G., Wigmore, S.J., Dejong, C.H.C., van Dam, R.M.: Prospective volumetric assessment of the liver on a personal computer by nonradiologists prior to partial hepatectomy. World Journal of Surgery 35(2), 386–392 (2011)
Dorcet, V., Larose, X., Fermin, C., Bissey, M., Boullay, P.: Extrax: an ImageJ plug-in for electron diffraction intensity extraction. Journal of Applied Crystallography 43(1), 191–195 (2010)
Federici, F., Dupuy, L., Laplaze, L., Heisler, M., Haseloff, J.: Integrated genetic and computation methods for in planta cytometry. Nature Methods 9(5), 483–485 (2012)
Kim, U.S., Kim, S.J., Baek, S.H., Kim, H.K., Sohn, Y.H.: Quantitative analysis of optic disc color. Korean Journal of Ophthalmology 25(3), 174–177 (2011)
Schmid, B., Helfrich-Förster, C., Yoshii, T.: A new ImageJ plug-in “ActogramJ” for chronobiological analyses. Journal of Biological Rhythms 26(5), 464–467 (2011)
Schneider, C.A., Rasband, W.S., Eliceiri, K.W.: NIH image to ImageJ: 25 years of image analysis. Nature Methods 9(7), 671–675 (2012)
Smith, M.B., Li, H., Shen, T., Huang, X., Yusuf, E., Vavylonis, D.: Segmentation and tracking of cytoskeletal filaments using open active contours. Cytoskeleton 67(11), 693–705 (2010)
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© 2014 Springer International Publishing Switzerland
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Czarnecki, W.M. (2014). InFeST – ImageJ Plugin for Rapid Development of Image Segmentation Pipelines. In: Gruca, D., Czachórski, T., Kozielski, S. (eds) Man-Machine Interactions 3. Advances in Intelligent Systems and Computing, vol 242. Springer, Cham. https://doi.org/10.1007/978-3-319-02309-0_30
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DOI: https://doi.org/10.1007/978-3-319-02309-0_30
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-02308-3
Online ISBN: 978-3-319-02309-0
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