title: ilastik: interactive machine learning for (bio)image analysis
creator: Berg, Stuart
creator: Kutra, Dominik
creator: Kroeger, Thorben
creator: Straehle, Christoph N.
creator: Kausler, Bernhard X.
creator: Haubold, Carsten
creator: Schiegg, Martin
creator: Ales, Janez
creator: Beier, Thorsten
creator: Rudy, Markus
creator: Eren, Kemal
creator: Cervantes, Jaime I
creator: Xu, Buote
creator: Beuttenmueller, Fynn
creator: Wolny, Adrian
creator: Zhang, Chong
creator: Koethe, Ullrich
creator: Hamprecht, Fred A.
creator: Kreshuk, Anna
subject: ddc-004
subject: 004 Data processing Computer science
subject: ddc-570
subject: 570 Life sciences
subject: ddc-600
subject: 600 Technology (Applied sciences)
description: We present ilastik, an easy-to-use interactive tool that brings machine-learning-based (bio)image analysis to end users without substantial computational expertise. It contains pre-defined workflows for image segmentation, object classification, counting and tracking. Users adapt the workflows to the problem at hand by interactively providing sparse training annotations for a nonlinear classifier. ilastik can process data in up to five dimensions (3D, time and number of channels). Its computational back end runs operations on-demand wherever possible, allowing for interactive prediction on data larger than RAM. Once the classifiers are trained, ilastik workflows can be applied to new data from the command line without further user interaction. We describe all ilastik workflows in detail, including three  case studies and a discussion on the expected performance.
publisher: Nature Publishing Group
date: 2019-09
type: Article
type: info:eu-repo/semantics/article
type: NonPeerReviewed
format: application/pdf
identifier: https://archiv.ub.uni-heidelberg.de/volltextserverhttps://archiv.ub.uni-heidelberg.de/volltextserver/28283/7/Berg_ilastik_2020.pdf
identifier: DOI:
identifier: urn:nbn:de:bsz:16-heidok-282831
identifier:   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  (2019) ilastik: interactive machine learning for (bio)image analysis.  Nature Methods, 2019 (16).  pp. 1-9.  ISSN 1548-7105 (Online-Ausg.), 1548-7091 (Druck-Ausg.)     
relation: https://archiv.ub.uni-heidelberg.de/volltextserver/28283/
rights: info:eu-repo/semantics/openAccess
rights: http://archiv.ub.uni-heidelberg.de/volltextserver/help/license_urhg.html
language: eng