Abstract
Segmentation is one of the most ubiquitous problems in biological image analysis. Here we present a machine learning-based solution to it as implemented in the open source ilastik toolkit. We give a broad description of the underlying theory and demonstrate two workflows: Pixel Classification and Autocontext. We illustrate their use on a challenging problem in electron microscopy image segmentation. After following this walk-through, we expect the readers to be able to apply the necessary steps to their own data and segment their images by either workflow.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Myers G (2012) Why bioimage informatics matters. Nat Methods 9(7):659–660
Meijering E, Carpenter AE, Peng H et al (2016) Imagining the future of bioimage analysis. Nat Biotechnol 34(12):1250–1255
Coelho L, Glory-Afshar E, Kangas J et al (2010) Principles of bioimage informatics: focus on machine learning of cell patterns. In: Blaschke C, Shatkay H (eds) ISBM/ECCB, 2010. Lecture notes in bioinformatics, vol 6004, pp 8–18
Sommer C, Gerlich D (2013) Machine learning in cell biology-teaching computers to recognize phenotypes. J Cell Sci 126(24):5529–5539
Kan A (2017) Machine learning applications in cell image analysis. Immunol Cell Biol 95:525–530
Sommer C, Straele C, Koethe U et al (2011) ilastik: interactive learning and segmentation toolkit. 8th IEEE International Symposium on Biomedical Imaging (ISBI). Proceedings, p 230–233
LeCun Y, Bengio Y, Hinton G (2015) Deep learning. Nature 521(7553):436–444
ilastik website (2018). www.ilastik.org/download
http://data.ilastik.org/ilastik_data_and_autocontext_project.zip
Breiman L (2001) Random forests. Mach Learn 45:5–32
Tu Z, Bai X (2009) Auto-context and its application to high-level vision tasks and 3D brain image segmentation. Trans Pattern Anal Mach Intelligence 32(10):1744–1757
Haubold C, Schiegg M, Kreshuk A et al (2016) Segmenting and tracking multiple dividing targets using ilastik. Focus on bio-image informatics, p 199–229
Straehle CN, Köthe U, Knott G et al (2011) Carving: scalable interactive segmentation of neural volume electron microscopy images. In: Fichtinger G, Martel A, Peters T (eds) Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2011. Lecture notes in computer science, vol 6891. Springer, Berlin Heidelberg, pp 653–660
Beier T, Pape C, Rahaman N et al (2017) Multicut brings automated neurite segmentation closer to human performance. Nat Methods 14(2):101–102
Arganda-Carreras I, Kaynig V, Rueden C et al (2017) Trainable Weka segmentation: a machine learning tool for microscopy pixel classification. Bioinformatics 33(15):2424–2426
Li X, Zhou Z, Keller P et al (2015) Interactive exemplar-based segmentation toolkit for biomedical image analysis. In: IEEE 12th International Symposium on Biomedical Imaging, p 168–171
Marée R, Rollus L, Stévens B et al (2016) Collaborative analysis of multi-gigapixel imaging data using Cytomine. Bioinformatics 32(9):1395–1401
Hilsenbeck O, Schwarzfischer M, Loeffler D et al (2017) fastER: a user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy. Bioinformatics 33(13):2020–2028
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Kreshuk, A., Zhang, C. (2019). Machine Learning: Advanced Image Segmentation Using ilastik. In: Rebollo, E., Bosch, M. (eds) Computer Optimized Microscopy. Methods in Molecular Biology, vol 2040. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9686-5_21
Download citation
DOI: https://doi.org/10.1007/978-1-4939-9686-5_21
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-4939-9685-8
Online ISBN: 978-1-4939-9686-5
eBook Packages: Springer Protocols