[{"publication_status":"published","keyword":["image segmentation","biomedical imaging","three dimensional displays","neurons","retina","observers","image color analysis"],"status":"public","type":"conference","extern":"1","oa":1,"abstract":[{"lang":"eng","text":"Segmentation is the process of partitioning digital images into meaningful regions. The analysis of biological high content images often requires segmentation as a first step. We propose ilastik as an easy-to-use tool which allows the user without expertise in image processing to perform segmentation and classification in a unified way. ilastik learns from labels provided by the user through a convenient mouse interface. Based on these labels, ilastik infers a problem specific segmentation. A random forest classifier is used in the learning step, in which each pixel's neighborhood is characterized by a set of generic (nonlinear) features. ilastik supports up to three spatial plus one spectral dimension and makes use of all dimensions in the feature calculation. ilastik provides realtime feedback that enables the user to interactively refine the segmentation result and hence further fine-tune the classifier. An uncertainty measure guides the user to ambiguous regions in the images. Real time performance is achieved by multi-threading which fully exploits the capabilities of modern multi-core machines. Once a classifier has been trained on a set of representative images, it can be exported and used to automatically process a very large number of images (e.g. using the CellProfiler pipeline). ilastik is an open source project and released under the BSD license at www.ilastik.org."}],"main_file_link":[{"open_access":"1","url":"https://www.researchgate.net/publication/224241106_Ilastik_Interactive_learning_and_segmentation_toolkit"}],"language":[{"iso":"eng"}],"date_created":"2021-08-19T11:49:58Z","oa_version":"Preprint","article_processing_charge":"No","_id":"9943","day":"09","conference":{"name":"ISBI: International Symposium on Biomedical Imaging","location":"Chicago, Illinois, USA","end_date":"2011-04-02","start_date":"2011-03-30"},"quality_controlled":"1","publication_identifier":{"issn":["1945-7928"],"isbn":["978-1-4244-4127-3"],"eissn":["1945-8452"]},"title":"Ilastik: Interactive learning and segmentation toolkit","publisher":"Institute of Electrical and Electronics Engineers","date_updated":"2023-02-23T14:13:38Z","year":"2011","publication":"2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro","author":[{"full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","first_name":"Christoph M","orcid":"0000-0003-1216-9105"},{"first_name":"Christoph","last_name":"Straehle","full_name":"Straehle, Christoph"},{"full_name":"Köthe, Ullrich","last_name":"Köthe","first_name":"Ullrich"},{"full_name":"Hamprecht, Fred A.","last_name":"Hamprecht","first_name":"Fred A."}],"doi":"10.1109/isbi.2011.5872394","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"06","department":[{"_id":"Bio"}],"date_published":"2011-06-09T00:00:00Z","citation":{"mla":"Sommer, Christoph M., et al. “Ilastik: Interactive Learning and Segmentation Toolkit.” <i>2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro</i>, Institute of Electrical and Electronics Engineers, 2011, doi:<a href=\"https://doi.org/10.1109/isbi.2011.5872394\">10.1109/isbi.2011.5872394</a>.","ieee":"C. M. Sommer, C. Straehle, U. Köthe, and F. A. Hamprecht, “Ilastik: Interactive learning and segmentation toolkit,” in <i>2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro</i>, Chicago, Illinois, USA, 2011.","short":"C.M. Sommer, C. Straehle, U. Köthe, F.A. Hamprecht, in:, 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro, Institute of Electrical and Electronics Engineers, 2011.","apa":"Sommer, C. M., Straehle, C., Köthe, U., &#38; Hamprecht, F. A. (2011). Ilastik: Interactive learning and segmentation toolkit. In <i>2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro</i>. Chicago, Illinois, USA: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/isbi.2011.5872394\">https://doi.org/10.1109/isbi.2011.5872394</a>","ista":"Sommer CM, Straehle C, Köthe U, Hamprecht FA. 2011. Ilastik: Interactive learning and segmentation toolkit. 2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro. ISBI: International Symposium on Biomedical Imaging.","ama":"Sommer CM, Straehle C, Köthe U, Hamprecht FA. Ilastik: Interactive learning and segmentation toolkit. In: <i>2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro</i>. Institute of Electrical and Electronics Engineers; 2011. doi:<a href=\"https://doi.org/10.1109/isbi.2011.5872394\">10.1109/isbi.2011.5872394</a>","chicago":"Sommer, Christoph M, Christoph Straehle, Ullrich Köthe, and Fred A. Hamprecht. “Ilastik: Interactive Learning and Segmentation Toolkit.” In <i>2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro</i>. Institute of Electrical and Electronics Engineers, 2011. <a href=\"https://doi.org/10.1109/isbi.2011.5872394\">https://doi.org/10.1109/isbi.2011.5872394</a>."}},{"quality_controlled":"1","article_processing_charge":"No","page":"331-355","language":[{"iso":"eng"}],"oa_version":"None","abstract":[{"text":"This chapter tackles a difficult challenge: presenting signal processing material to non-experts. This chapter is meant to be comprehensible to people who have some math background, including a course in linear algebra and basic statistics, but do not specialize in mathematics, engineering, or related fields. Some formulas assume the reader is familiar with matrices and basic matrix operations, but not more advanced material. Furthermore, we tried to make the chapter readable even if you skip the formulas. Nevertheless, we include some simple methods to demonstrate the basics of adaptive data processing, then we proceed with some advanced methods that are fundamental in adaptive signal processing, and are likely to be useful in a variety of applications. The advanced algorithms are also online available [30]. In the second part, these techniques are applied to some real-world BCI data.","lang":"eng"}],"status":"public","type":"book_chapter","alternative_title":["The Frontiers Collection"],"date_published":"2010-09-06T00:00:00Z","acknowledgement":"This work was supported by the EU grants “BrainCom” (FP6-2004-Mobility-5 Grant No 024259) and “Multi-adaptive BCI” (MEIF-CT-2006 Grant No 040666). Furthermore, we thank Matthias Krauledat for fruitful discussions and tools for generating Fig. 5.","department":[{"_id":"ScienComp"}],"scopus_import":"1","series_title":"FRONTCOLL","place":"Berlin, Heidelberg","_id":"14983","day":"06","date_created":"2024-02-14T09:56:00Z","edition":"1","publication_status":"published","citation":{"ama":"Schlögl A, Vidaurre C, Müller K-R. Adaptive Methods in BCI Research - An Introductory Tutorial. In: Graimann B, Pfurtscheller G, Allison B, eds. <i>Brain-Computer Interfaces</i>. 1st ed. FRONTCOLL. Berlin, Heidelberg: Springer; 2010:331-355. doi:<a href=\"https://doi.org/10.1007/978-3-642-02091-9_18\">10.1007/978-3-642-02091-9_18</a>","chicago":"Schlögl, Alois, Carmen Vidaurre, and Klaus-Robert Müller. “Adaptive Methods in BCI Research - An Introductory Tutorial.” In <i>Brain-Computer Interfaces</i>, edited by Bernhard Graimann, Gert Pfurtscheller, and Brendan Allison, 1st ed., 331–55. FRONTCOLL. Berlin, Heidelberg: Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-02091-9_18\">https://doi.org/10.1007/978-3-642-02091-9_18</a>.","ista":"Schlögl A, Vidaurre C, Müller K-R. 2010.Adaptive Methods in BCI Research - An Introductory Tutorial. In: Brain-Computer Interfaces. The Frontiers Collection, , 331–355.","apa":"Schlögl, A., Vidaurre, C., &#38; Müller, K.-R. (2010). Adaptive Methods in BCI Research - An Introductory Tutorial. In B. Graimann, G. Pfurtscheller, &#38; B. Allison (Eds.), <i>Brain-Computer Interfaces</i> (1st ed., pp. 331–355). Berlin, Heidelberg: Springer. <a href=\"https://doi.org/10.1007/978-3-642-02091-9_18\">https://doi.org/10.1007/978-3-642-02091-9_18</a>","short":"A. Schlögl, C. Vidaurre, K.-R. Müller, in:, B. Graimann, G. Pfurtscheller, B. Allison (Eds.), Brain-Computer Interfaces, 1st ed., Springer, Berlin, Heidelberg, 2010, pp. 331–355.","mla":"Schlögl, Alois, et al. “Adaptive Methods in BCI Research - An Introductory Tutorial.” <i>Brain-Computer Interfaces</i>, edited by Bernhard Graimann et al., 1st ed., Springer, 2010, pp. 331–55, doi:<a href=\"https://doi.org/10.1007/978-3-642-02091-9_18\">10.1007/978-3-642-02091-9_18</a>.","ieee":"A. Schlögl, C. Vidaurre, and K.-R. Müller, “Adaptive Methods in BCI Research - An Introductory Tutorial,” in <i>Brain-Computer Interfaces</i>, 1st ed., B. Graimann, G. Pfurtscheller, and B. Allison, Eds. Berlin, Heidelberg: Springer, 2010, pp. 331–355."},"author":[{"last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois","first_name":"Alois","orcid":"0000-0002-5621-8100"},{"full_name":"Vidaurre, Carmen","last_name":"Vidaurre","first_name":"Carmen"},{"last_name":"Müller","full_name":"Müller, Klaus-Robert","first_name":"Klaus-Robert"}],"doi":"10.1007/978-3-642-02091-9_18","month":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Brain-Computer Interfaces","publisher":"Springer","date_updated":"2024-10-21T06:03:06Z","corr_author":"1","year":"2010","publication_identifier":{"eisbn":["9783642020919"],"isbn":["9783642020902"],"issn":["1612-3018"]},"title":"Adaptive Methods in BCI Research - An Introductory Tutorial","editor":[{"first_name":"Bernhard","last_name":"Graimann","full_name":"Graimann, Bernhard"},{"full_name":"Pfurtscheller, Gert","last_name":"Pfurtscheller","first_name":"Gert"},{"first_name":"Brendan","last_name":"Allison","full_name":"Allison, Brendan"}]},{"pmid":1,"date_published":"2010-08-18T00:00:00Z","scopus_import":"1","isi":1,"department":[{"_id":"Bio"},{"_id":"CaHe"}],"type":"journal_article","status":"public","volume":29,"intvolume":"        29","article_processing_charge":"No","quality_controlled":"1","abstract":[{"text":"Integrin- and cadherin-mediated adhesion is central for cell and tissue morphogenesis, allowing cells and tissues to change shape without loosing integrity. Studies predominantly in cell culture showed that mechanosensation through adhesion structures is achieved by force-mediated modulation of their molecular composition. The specific molecular composition of adhesion sites in turn determines their signalling activity and dynamic reorganization. Here, we will review how adhesion sites respond to mecanical stimuli, and how spatially and temporally regulated signalling from different adhesion sites controls cell migration and tissue morphogenesis.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2924654/"}],"language":[{"iso":"eng"}],"page":"2753 - 2768","oa_version":"Submitted Version","publisher":"Wiley-Blackwell","date_updated":"2025-09-30T09:29:30Z","year":"2010","publication":"EMBO Journal","title":"Spatial organization of adhesion: force-dependent regulation and function in tissue morphogenesis","acknowledged_ssus":[{"_id":"Bio"}],"citation":{"short":"E. Papusheva, C.-P.J. Heisenberg, EMBO Journal 29 (2010) 2753–2768.","apa":"Papusheva, E., &#38; Heisenberg, C.-P. J. (2010). Spatial organization of adhesion: force-dependent regulation and function in tissue morphogenesis. <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1038/emboj.2010.182\">https://doi.org/10.1038/emboj.2010.182</a>","ieee":"E. Papusheva and C.-P. J. Heisenberg, “Spatial organization of adhesion: force-dependent regulation and function in tissue morphogenesis,” <i>EMBO Journal</i>, vol. 29, no. 16. Wiley-Blackwell, pp. 2753–2768, 2010.","mla":"Papusheva, Ekaterina, and Carl-Philipp J. Heisenberg. “Spatial Organization of Adhesion: Force-Dependent Regulation and Function in Tissue Morphogenesis.” <i>EMBO Journal</i>, vol. 29, no. 16, Wiley-Blackwell, 2010, pp. 2753–68, doi:<a href=\"https://doi.org/10.1038/emboj.2010.182\">10.1038/emboj.2010.182</a>.","chicago":"Papusheva, Ekaterina, and Carl-Philipp J Heisenberg. “Spatial Organization of Adhesion: Force-Dependent Regulation and Function in Tissue Morphogenesis.” <i>EMBO Journal</i>. Wiley-Blackwell, 2010. <a href=\"https://doi.org/10.1038/emboj.2010.182\">https://doi.org/10.1038/emboj.2010.182</a>.","ama":"Papusheva E, Heisenberg C-PJ. Spatial organization of adhesion: force-dependent regulation and function in tissue morphogenesis. <i>EMBO Journal</i>. 2010;29(16):2753-2768. doi:<a href=\"https://doi.org/10.1038/emboj.2010.182\">10.1038/emboj.2010.182</a>","ista":"Papusheva E, Heisenberg C-PJ. 2010. Spatial organization of adhesion: force-dependent regulation and function in tissue morphogenesis. EMBO Journal. 29(16), 2753–2768."},"external_id":{"isi":["000281006400009"],"pmid":["20717145"]},"doi":"10.1038/emboj.2010.182","publist_id":"1962","author":[{"last_name":"Papusheva","id":"41DB591E-F248-11E8-B48F-1D18A9856A87","full_name":"Papusheva, Ekaterina","first_name":"Ekaterina"},{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg"}],"month":"08","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","issue":"16","_id":"4157","day":"18","oa":1,"date_created":"2018-12-11T12:07:17Z"}]