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 |
| Repository | |
| 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[edit]
ilastik allows user to annotate an arbitrary number of classes in images with a mouse interface. Using these user annotations and the generic (nonlinear[disambiguation needed]) 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[edit]
ilastik was first released in 2011 by scientists at the Heidelberg Collaboratory for Image Processing (HCI), University of Heidelberg.
Application[edit]
- The Interactive Learning and Segmentation Toolkit
- Carving[2][3]
- Cell classification and neuron classification[4]
- Synapse detection
- Cell tracking[5]
Resources[edit]
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[edit]
- ^ 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. S2CID 206949135.
- ^ 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; Straehle CN; Sommer C; Koethe U; Cantoni M; et al. (2011). "Automated Detection and Segmentation of Synaptic Contacts in Nearly Isotropic Serial Electron Microscopy Images". PLOS ONE. 6 (10): e24899. Bibcode:2011PLoSO...624899K. doi:10.1371/journal.pone.0024899. PMC 3198725. PMID 22031814.
- ^ Berg, Stuart; Kutra, Dominik; Kroeger, Thorben; Straehle, Christoph N.; Kausler, Bernhard X.; Haubold, Carsten; Schiegg, Martin; Ales, Janez; Beier, Thorsten; Rudy, Markus; Eren, Kemal; Cervantes, Jaime I; Xu, Buote; Beuttenmueller, Fynn; Wolny, Adrian; Zhang, Chong; Koethe, Ullrich; Hamprecht, Fred A.; Kreshuk, Anna (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. S2CID 203609613.
