ilastik: interactive machine learning for (bio)image analysis
Stuart Berg
1
,
Dominik Kutra
2, 3
,
Thorben Kroeger
2
,
Christoph N Straehle
2
,
Bernhard X. Kausler
2
,
Carsten Haubold
2
,
Martin Schiegg
2
,
Janez Ales
2
,
Thorsten Beier
2
,
Markus Rudy
2
,
Kemal Eren
2
,
Jaime I. Cervantes
2
,
Buote Xu
2
,
Fynn Beuttenmueller
2, 3
,
Adrian Wolny
2
,
Chong Zhang
2
,
Ullrich Koethe
2
,
Fred A. Hamprecht
2
,
Anna Kreshuk
2, 3
Publication type: Journal Article
Publication date: 2019-09-30
scimago Q1
wos Q1
SJR: 17.251
CiteScore: 49.0
Impact factor: 32.1
ISSN: 15487091, 15487105
PubMed ID:
31570887
Biochemistry
Molecular Biology
Cell Biology
Biotechnology
Abstract
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. ilastik is an user-friendly interactive tool for machine-learning-based image segmentation, object classification, counting and tracking.
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GOST
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Berg S. et al. ilastik: interactive machine learning for (bio)image analysis // Nature Methods. 2019. Vol. 16. No. 12. pp. 1226-1232.
GOST all authors (up to 50)
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Berg S., Kutra D., Kroeger T., Straehle C. N., Kausler B. X., Haubold C., Schiegg M., Ales J., Beier T., Rudy M., Eren K., Cervantes J. I., Xu B., Beuttenmueller F., Wolny A., Zhang C., Koethe U., Hamprecht F. A., Kreshuk A. ilastik: interactive machine learning for (bio)image analysis // Nature Methods. 2019. Vol. 16. No. 12. pp. 1226-1232.
Cite this
RIS
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TY - JOUR
DO - 10.1038/s41592-019-0582-9
UR - https://doi.org/10.1038/s41592-019-0582-9
TI - ilastik: interactive machine learning for (bio)image analysis
T2 - Nature Methods
AU - Berg, Stuart
AU - Kutra, Dominik
AU - Kroeger, Thorben
AU - Straehle, Christoph N
AU - Kausler, Bernhard X.
AU - Haubold, Carsten
AU - Schiegg, Martin
AU - Ales, Janez
AU - Beier, Thorsten
AU - Rudy, Markus
AU - Eren, Kemal
AU - Cervantes, Jaime I.
AU - Xu, Buote
AU - Beuttenmueller, Fynn
AU - Wolny, Adrian
AU - Zhang, Chong
AU - Koethe, Ullrich
AU - Hamprecht, Fred A.
AU - Kreshuk, Anna
PY - 2019
DA - 2019/09/30
PB - Springer Nature
SP - 1226-1232
IS - 12
VL - 16
PMID - 31570887
SN - 1548-7091
SN - 1548-7105
ER -
Cite this
BibTex (up to 50 authors)
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@article{2019_Berg,
author = {Stuart Berg and Dominik Kutra and Thorben Kroeger and Christoph N Straehle and Bernhard X. Kausler and Carsten Haubold and Martin Schiegg and Janez Ales and Thorsten Beier and Markus Rudy and Kemal Eren and Jaime I. Cervantes and Buote Xu and Fynn Beuttenmueller and Adrian Wolny and Chong Zhang and Ullrich Koethe and Fred A. Hamprecht and Anna Kreshuk},
title = {ilastik: interactive machine learning for (bio)image analysis},
journal = {Nature Methods},
year = {2019},
volume = {16},
publisher = {Springer Nature},
month = {sep},
url = {https://doi.org/10.1038/s41592-019-0582-9},
number = {12},
pages = {1226--1232},
doi = {10.1038/s41592-019-0582-9}
}
Cite this
MLA
Copy
Berg, Stuart, et al. “ilastik: interactive machine learning for (bio)image analysis.” Nature Methods, vol. 16, no. 12, Sep. 2019, pp. 1226-1232. https://doi.org/10.1038/s41592-019-0582-9.