---
_id: '9943'
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.
article_processing_charge: No
author:
- first_name: Christoph M
  full_name: Sommer, Christoph M
  id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
  last_name: Sommer
  orcid: 0000-0003-1216-9105
- first_name: Christoph
  full_name: Straehle, Christoph
  last_name: Straehle
- first_name: Ullrich
  full_name: Köthe, Ullrich
  last_name: Köthe
- first_name: Fred A.
  full_name: Hamprecht, Fred A.
  last_name: Hamprecht
citation:
  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>'
  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>'
  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>.'
  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.'
  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.'
  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>.'
  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.'
conference:
  end_date: 2011-04-02
  location: Chicago, Illinois, USA
  name: 'ISBI: International Symposium on Biomedical Imaging'
  start_date: 2011-03-30
date_created: 2021-08-19T11:49:58Z
date_published: 2011-06-09T00:00:00Z
date_updated: 2023-02-23T14:13:38Z
day: '09'
department:
- _id: Bio
doi: 10.1109/isbi.2011.5872394
extern: '1'
keyword:
- image segmentation
- biomedical imaging
- three dimensional displays
- neurons
- retina
- observers
- image color analysis
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.researchgate.net/publication/224241106_Ilastik_Interactive_learning_and_segmentation_toolkit
month: '06'
oa: 1
oa_version: Preprint
publication: '2011 IEEE International Symposium on Biomedical Imaging: from Nano to
  Micro'
publication_identifier:
  eissn:
  - 1945-8452
  isbn:
  - 978-1-4244-4127-3
  issn:
  - 1945-7928
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
status: public
title: 'Ilastik: Interactive learning and segmentation toolkit'
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2011'
...