---
_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'
...
---
_id: '14983'
abstract:
- lang: eng
  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.'
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.
alternative_title:
- The Frontiers Collection
article_processing_charge: No
author:
- first_name: Alois
  full_name: Schlögl, Alois
  id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
  last_name: Schlögl
  orcid: 0000-0002-5621-8100
- first_name: Carmen
  full_name: Vidaurre, Carmen
  last_name: Vidaurre
- first_name: Klaus-Robert
  full_name: Müller, Klaus-Robert
  last_name: Müller
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>'
  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>'
  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>.'
  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.'
  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.'
  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>.
  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.
corr_author: '1'
date_created: 2024-02-14T09:56:00Z
date_published: 2010-09-06T00:00:00Z
date_updated: 2024-10-21T06:03:06Z
day: '06'
department:
- _id: ScienComp
doi: 10.1007/978-3-642-02091-9_18
edition: '1'
editor:
- first_name: Bernhard
  full_name: Graimann, Bernhard
  last_name: Graimann
- first_name: Gert
  full_name: Pfurtscheller, Gert
  last_name: Pfurtscheller
- first_name: Brendan
  full_name: Allison, Brendan
  last_name: Allison
language:
- iso: eng
month: '09'
oa_version: None
page: 331-355
place: Berlin, Heidelberg
publication: Brain-Computer Interfaces
publication_identifier:
  eisbn:
  - '9783642020919'
  isbn:
  - '9783642020902'
  issn:
  - 1612-3018
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
series_title: FRONTCOLL
status: public
title: Adaptive Methods in BCI Research - An Introductory Tutorial
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '4157'
abstract:
- lang: eng
  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.
acknowledged_ssus:
- _id: Bio
article_processing_charge: No
author:
- first_name: Ekaterina
  full_name: Papusheva, Ekaterina
  id: 41DB591E-F248-11E8-B48F-1D18A9856A87
  last_name: Papusheva
- first_name: Carl-Philipp J
  full_name: Heisenberg, Carl-Philipp J
  id: 39427864-F248-11E8-B48F-1D18A9856A87
  last_name: Heisenberg
  orcid: 0000-0002-0912-4566
citation:
  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>'
  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>'
  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>.'
  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.'
  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.'
  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>.'
  short: E. Papusheva, C.-P.J. Heisenberg, EMBO Journal 29 (2010) 2753–2768.
date_created: 2018-12-11T12:07:17Z
date_published: 2010-08-18T00:00:00Z
date_updated: 2025-09-30T09:29:30Z
day: '18'
department:
- _id: Bio
- _id: CaHe
doi: 10.1038/emboj.2010.182
external_id:
  isi:
  - '000281006400009'
  pmid:
  - '20717145'
intvolume: '        29'
isi: 1
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2924654/
month: '08'
oa: 1
oa_version: Submitted Version
page: 2753 - 2768
pmid: 1
publication: EMBO Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '1962'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Spatial organization of adhesion: force-dependent regulation and function
  in tissue morphogenesis'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 29
year: '2010'
...