Software:ilastik
| Developer(s) | Christoph Sommer, Christoph Straehle, Thorben Kröger, Bernhard X. Kausler, Ullrich Koethe, Fred A. Hamprecht, Anna Kreshuk and others |
|---|---|
| Initial release | 2011 |
| Stable release | 1.3.3
/ October 7, 2019 |
| Operating system | Any (Python based) |
| Type | Image processing & Computer vision & Machine Learning |
| License | GPL2 |
| Website | www |
Ilastik[1] is a user-friendly free open source software for image classification and segmentation. No previous experience in image processing is required to run the software.
Features
ilastik allows user to annotate an arbitrary number of classes in images with a mouse interface. Using these user annotations and the generic (nonlinear) image features, the user can train a random forest classifier. ilastik has a CellProfiler module to use ilastik classifiers to process images within a CellProfiler framework.
History
ilastik was first released in 2011 by scientists at the Heidelberg Collaboratory for Image Processing (HCI), University of Heidelberg.
Application
- The Interactive Learning and Segmentation Toolkit
- Carving[2][3]
- Cell classification and neuron classification[4]
- Synapse detection
- Cell tracking[5]
Resources
ilastik project is hosted on GitHub. It is a collaborative project, any contributions such as comments, bug reports, bug fixes or code contributions are welcome.
References
- ↑ Sommer, C; Straehle C; Koethe U; Hamprecht FA (2011). "Ilastik: Interactive learning and segmentation toolkit". 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Macro. pp. 230–33. doi:10.1109/ISBI.2011.5872394. ISBN 978-1-4244-4127-3.
- ↑ Straehle, C; Köthe U; Briggman K; Denk W; Hamprecht FA (2012). "Seeded watershed cut uncertainty estimators for guided interactive segmentation". CVPR.
- ↑ Straehle, CN; Köthe U; Knott G; Hamprecht FA (2011). "Carving: scalable interactive segmentation of neural volume electron microscopy images". MICCAI 14 (Pt 1): 653–60. doi:10.1007/978-3-642-23623-5_82. PMID 22003674.
- ↑ Kreshuk, A et al. (2011). "Automated Detection and Segmentation of Synaptic Contacts in Nearly Isotropic Serial Electron Microscopy Images". PLOS ONE 6 (10): e24899. doi:10.1371/journal.pone.0024899. PMID 22031814. Bibcode: 2011PLoSO...624899K.
- ↑ Berg, Stuart; Kutra, Dominik; Kroeger, Thorben; Straehle, Christoph N.; Kausler, Bernhard X.; Haubold, Carsten; Schiegg, Martin; Ales, Janez et al. (30 September 2019). "ilastik: interactive machine learning for (bio)image analysis". Nature Methods 16 (12): 1226–1232. doi:10.1038/s41592-019-0582-9. PMID 31570887. https://zenodo.org/record/3795652.
External links
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