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publications.html
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---
layout: default
title: Publications
category: "Publications"
---
<div class="row">
<div class="col-sm-3">
<ul class="sidenav nav nav-list well" data-offset-top="130">
<li><a href="#cite">How to cite</a></li>
<li><a href="#reviews">Reviews</a></li>
<li><a href="#others">Applications by ilastik users</a></li>
<li><a href="#ours">Applications by ilastik developers</a></li>
</ul>
</div>
<div class="col-sm-9">
<p>
<b>How to cite:</b>
This conference paper describes the first release of ilastik (version 0.5):
<ul>
<li>
<em>ilastik: Interactive Learning and Segmentation Toolkit</em><br>
C. Sommer, C. Strähle, U. Köthe, F. A. Hamprecht<br>
in: Eighth IEEE International Symposium on Biomedical Imaging (ISBI). Proceedings, (2011), 230-233 <br>
<a href="http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5872394&tag=1">Link at publisher</a>,
<a href="http://hci.iwr.uni-heidelberg.de/MIP/Publications/getbibfile.php?id=58914">BibTex file</a>,
<a href="http://hci.iwr.uni-heidelberg.de/publications/mip/techrep/sommer_11_ilastik.pdf">
Technical Report</a>
</li>
</ul>
</p>
<p>
<b id="reviews">Reviews:</b>
Many colleagues have been so kind as to include ilastik into their reviews of image processing software.
If you want to get a better idea of how ilastik compares with similar software tools in different application
domains, read one of the references below:
<ul>
<li><em>Machine learning applications in cell image analysis</em><br>
Andrey Kan<br>
Immunology and Cell Biology, 2017
</li>
<li><em>High-Content Screening for Quantitative Cell Biology</em><br>
Mojca Mattiazzi Usaj, Erin B. Styles, Adrian J. Verster, Helena Friesen, Charles Boone and Brenda J. Andrews <br>
Trends in Cell Biology, 2016
</li>
<li><em>Exploring the third dimension: Volume electron microscopy comes of age</em><br>
C.J. Peddie, L.M. Collinson<br>
Micron, 2014
</li>
<li><em>Automated Processing of Zebrafish Imaging Data: A Survey </em><br>
R. Mikut, T. Dickmeis, W. Driever, P. Geurts, F.A. Hamprecht, <br>
B.X. Kausler, M.J. Ledesma-Carbayo, R. Marée, K. Mikula, <br>
P. Pantazis, O. Ronneberger, A. Santos, R. Stotzka, <br>
U. Straehle, and N. Peyriéras <br>
Zebrafish, September 2013, 10(3): 401-421.
</li>
<li><em> Bioimage Informatics for Systems Pharmacology</em><br>
F. Li, Z. Yin, G. Jin, H. Zhao, S.T.C. Wong <br>
PLoS computational biology, 2013
</li>
<li><em>Light microscopy applications in systems biology: opportunities and challenges</em><br>
P.M.A. Antony, C. Trefois, A. Stojanovic, A.S. Baumuratov, K. Kozak <br>
Cell Communication and Signaling, 2013, 11:24
</li>
<li><em>Computational methods and challenges for large-scale circuit mapping</em><br>
M. Helmstaedter, P.P. Mitra<br>
Current opinion in neurobiology, 2012
</li>
<li><em> A call for bioimaging software usability</em><br>
A.E. Carpenter, L. Kamentsky, K.W. Eliceiri<br>
Nature methods, 2012
</li>
</ul>
</p>
<p>
<b id="others">Applications by ilastik users</b>:
Researchers from various application domains have successfully used ilastik in their work.
An almost random selection of such papers is shown below, see
<a href=https://scholar.google.com/scholar?cites=8459688359110226056&as_sdt=2005&sciodt=0,5&hl=en>
google scholar</a> for the full listing.
<ul>
<li><em>High-avidity IgA protects the intestine by enchaining growing bacteria</em><br>
Kathrin Moor, Médéric Diard, Mikael E. Sellin, Boas Felmy, Sandra Y. Wotzka, Albulena Toska, Erik Bakkeren,
Markus Arnoldini, Florence Bansept, Alma Dal Co, Tom Völler, Andrea Minola, Blanca Fernandez-Rodriguez, Gloria Agatic,
Sonia Barbieri, Luca Piccoli, Costanza Casiraghi, Davide Corti, Antonio Lanzavecchia, Roland R. Regoes, Claude Loverdo, Roman Stocker,
Douglas R. Brumley, Wolf-Dietrich Hardt, Emma Slack <br>
Nature (2017), Vol. 544
</li>
<li><em>Increased spatiotemporal resolution reveals highly dynamic dense tubular matrices in the peripheral ER </em><br>
Jonathon Nixon-Abell, Christopher J. Obara, Aubrey V. Weigel, Dong Li, Wesley R. Legant, C. Shan Xu, H. Amalia Pasolli, Kirsten Harvey,
Harald F. Hess, Eric Betzig, Craig Blackstone, Jennifer Lippincott-Schwartz <br>
Science (2016), Vol. 354, Issue 6311
</li>
<li><em>Mapping of Brain Activity by Automated Volume Analysis of Immediate Early Genes</em><br>
Nicolas Renier, Eliza L. Adams, Christoph Kirst, Zhuhao Wu, Ricardo Azevedo, Johannes Kohl, Anita E. Autry, Lolahon Kadiri,
Kannan Umadevi Venkataraju, Yu Zhou, Victoria X. Wang, Cheuk Y. Tang, Olav Olsen, Catherine Dulac, Pavel Osten, Marc Tessier-Lavigne<br>
Cell (2016), Volume 165, Issue 7
</li>
<li><em>High-throughput estimation of incident light, light interception and radiation-use efficiency of thousands of plants in a phenotyping platform</em><br>
Llorenc Cabrera-Bosquet, Christian Fournier, Nicolas Brichet, Claude Welcker, Benoit Suard and Francois Tardieu<br>
New Phytologist (2016)
</li>
<li>Static Clathrin Assemblies at the Peripheral Vacuole—Plasma Membrane Interface of the Parasitic Protozoan Giardia lamblia</em><br>
Jon Paulin Zumthor, Lenka Cernikova, Samuel Rout, Andres Kaech, Carmen Faso, Adrian B. Hehl <br>
PLoS Pathogens (2016)
</li>
<li><em>PIK3CAH1047R induces multipotency and multi-lineage mammary tumours</em><br>
Shany Koren, Linsey Reavie, Joana Pinto Couto, Duvini De Silva, Michael B. Stadler, Tim Roloff, Adrian Britschgi, Tobias Eichlisberger,
Hubertus Kohler, Olulanu Aina, Robert D. Cardiff & Mohamed Bentires-Alj<br>
Nature (2015), 525, 114–118
</li>
<li><em>Dopamine neurons projecting to the posterior striatum form an anatomically distinct subclass</em><br>
William Menegas, Joseph F. Bergan, Sachie K. Ogawa, Yoh Isogai, Kannan Umadevi Venkataraju,
Pavel Osten, Naoshige Uchida and Mitsuko Watabe-Uchida<br>
Elife (2015)
</li>
<li><em>Spatial constraints control cell proliferation in tissues</em><br>
Sebastian J. Streichan, Christian R. Hoerner, Tatjana Schneidt, Daniela Holzer and Lars Hufnagel<br>
PNAS (2014), vol. 111 no. 15
</li>
<li><em>Fast and robust optical flow for time-lapse microscopy using super-voxels</em><br>
F. Amat, E.W. Myers, P.J. Keller<br>
Bioinformatics (2013) 29 (3): 373-380
</li>
<li><em>Tubular endocytosis drives remodelling of the apical surface during epithelial morphogenesis in Drosophila</em><br>
P. Fabrowski, A.S. Necakov, S. Mumbauer, E. Loeser, A. Reversi, S. Streichan, J.A.G. Briggs, S. De Renzis<br>
Nature Communications 4 (2013), Article number: 2244
</li>
<li><em>Analyzing the footprints of near-surface aqueous turbulence: An image processing-based approach</em><br>
J. Schnieders, C.S. Garbe, W.L. Peirson, G.B. Smith, C.J. Zappa<br>
Journal of Geophysical Research: Oceans (2013), Vol 118 Issue 3
</li>
<li><em>Drop swarm analysis in dispersions with incident-light and transmitted-light illumination</em><br>
M. Mickler, B. Boecker, H.-J. Bart<br>
Flow Measurement and Instrumentation (2013), Vol. 30
</li>
<li><em>Heterogeneous Nanoscale Morphology in Cross-Sections of Bulk Heterojunction <br>
Polymer Solar Cells Visualized by Analytical Electron Microscopy</em><br>
Harald Flügge,Martin Pfannmöller, Gerd Benner, Irene Wacker, Hans Schmidt, <br>
Torsten Rabe, Rasmus R. Schröder, Wolfgang Kowalsky<br>
Energy Procedia, Volume 31, (2012), 46–59
</li>
<li><em>Minimizing Manual Image Segmentation Turn-Around Time for Neuronal Reconstruction by Embracing Uncertainty </em><br>
S.M. Plaza, L.K. Scheffer, M. Saunders<br>
PLoS ONE 7(9): e44448. (2013) doi:10.1371/journal.pone.0044448
</li>
<li><em> Efficient fluorescence image normalization for time lapse movies</em><br>
M. Schwarzfischer,C. Marr,J. Krumsiek,P. Hoppe,T. Schroeder,F. Theis<br>
In Proc. Microscopic Image Analysis with Applications in Biology (2011)
</li>
<li><em>Mechanical stiffness as an improved single-cell indicator of osteoblastic human <br>
mesenchymal stem cell differentiation</em><br>
T. Bongiorno, J. Kazlow, R. Mezencev, S. Griffiths, R. Olivares-Navarrete, J.F. McDonald, Z. Schwartz, <br>
B.D. Boyan, T.C. McDevitt, T. Sulchek<br>
Journal of Biomechanics (2013), in press
</li>
<li><em>Optimized Signal Separation for 3D-Polarized Light Imaging</em><br>
J. Dammers, L. Breuer, G. Tabbì, M. Axer<br>
Functional Brain Mapping and the Endeavor to Understand the Working Brain, (2013)
</li>
<li><em>The Flavonoid Isoquercitrin Promotes Neurite Elongation by Reducing RhoA Activity</em><br>
G. Palazzolo, P. Horvath, M. Zenobi-Wong <br>
PLoS ONE 7(11): e49979. (2011)
</li>
</ul>
</p>
<p>
<b id="ours">Applications by ilastik developers</b>:
Our developers themselves use ilastik in the course of their research
and try their best to build their new algorithms into ilastik to make
them available to non-experts. Some of their ilastik-related work is listed
below, grouped by the application field:
<dl>
<dt>Neuroscience</dt>
<dd>
<ul>
<li>
<em>Automated Detection of Synapses in Serial Section Transmission Electron Microscopy Image Stacks</em><br>
A. Kreshuk, U. Köthe, E. Pax, D. D. Bock, F. A. Hamprecht<br>
PLoS ONE, in press, (2014)
</li>
<li>
<em>Learning to Segment Neurons with Non-local Quality Measures</em><br>
T. Kröger, S. Mikula, W. Denk, U. Köthe, F. A. Hamprecht<br>
in: MICCAI 2013. Proceedings, part II, Springer(2013) 8150, 419-427
</li>
<li>
<em>Correlative in vivo 2 photon and focused ion beam scanning electron microscopy of cortical neurons</em><br>
B. Maco, A. Holtmaat, M. Cantoni, A. Kreshuk, C. N. Straehle, F. A. Hamprecht, G. W. Knott<br>
PloS ONE, (2013) 8 (2)
</li>
<li>
<em>Globally Optimal Closed-Surface Segmentation for Connectomics</em><br>
B. Andres, T. Kröger, K. L. Briggmann, W. Denk, N. Norogod, G. Knott, U. Köthe, F. A. Hamprecht<br>
in: ECCV 2012. Proceedings, Part 3, (2012), 778-791
</li>
<li>
<em>3D Segmentation of SBFSEM Images of Neuropil by a Graphical Model over Supervoxel Boundaries</em><br>
B. Andres, U. Köthe, T. Kröger, M. Helmstaedter, K.L. Briggman, W. Denk, F. A. Hamprecht<br>
Medical Image Analysis, (2012) 16 (2012), 796-805
</li>
<li>
<em>Seeded watershed cut uncertainty estimators for guided interactive segmentation</em> <br>
C. Straehle, U. Köthe, K. Briggman, W. Denk, F.A. Hamprecht<br>
in: CVPR 2012. Proceedings, (2012), 765 - 772
</li>
<li>
<em>Automated Detection and Segmentation of Synaptic Contacts in Nearly Isotropic Serial Electron Microscopy Images</em><br>
A. Kreshuk, C. N. Straehle, C. Sommer, U. Köthe, M. Cantoni, G. Knott, F. A. Hamprecht<br>
PLoS ONE, (2011) 6 (10)
</li>
<li>
<em>Carving: Scalable Interactive Segmentation of Neural Volume Electron Microscopy Images</em><br>
C. N. Straehle, U. Köthe, G. Knott, F. A. Hamprecht<br>
in: MICCAI 2011, Proceedings., Springer(2011) 6891, 653-660
<li>
<em>Automated Segmentation of Synapses in 3D EM Data</em><br>
A. Kreshuk, C. Strähle, C. Sommer, U. Köthe, G. Knott, F. A. Hamprecht<br>
in: Eighth IEEE International Symposium on Biomedical Imaging (ISBI). Proceedings, (2011), 220-223 <br>
</li>
</ul>
</dd>
</dt>
<dt>Cell Tracking</dt>
<dd>
<ul>
<li>
<em>Conservation Tracking</em><br>
M. Schiegg, P. Hanslovsky, B. X. Kausler, L. Hufnagel, F. A. Hamprecht<br>
in: ICCV 2013. Proceedings, (2013), 2928--2935
</li>
<li>
<em>A Discrete Chain Graph Model for 3d+t Cell Tracking with High Misdetection Robustness</em><br>
B. X. Kausler, M. Schiegg, B. Andres, M. Lindner, U. Köthe, H. Leitte, J. Wittbrodt, L. Hufnagel, F. A. Hamprecht<br>
in: ECCV 2012. Proceedings, Part 3, (2012) 7574, 144-157
</li>
</ul>
</dd>
<dt>Counting w/o detection</dt>
<dd>
<ul>
<li><em>Learning to Count with Regression Forest and Structured Labels</em><br>
L. Fiaschi, R. Nair, U. Köthe, F. A. Hamprecht <br>
ICPR 2012. Proceedings, (2012), 2685-2688
</li>
</ul>
</dd>
<dt>Cell detection</dt>
<dd>
<ul>
<li><em>Yeast Cell Detection and Segmentation in Bright Field Microscopy</em><br>
C. Zhang, F. Huber, M. Knop, F. A. Hamprecht<br>
in: ISBI 2014. Proceedings, in press, (2014)
</li>
<li><em>Learning-based Mitotic Cell Detection in Histopathological Images</em><br>
C. Sommer, L. Fiaschi, F. A. Hamprecht, D. Gerlich<br>
ICPR 2012. Proceedings, (2012), 2306-2309 <br>
</li>
<li><em>Keeping count: Leveraging temporal context to count heavily overlapping objects </em><br>
L. Fiaschi, G. Konstantin, B. Afonso, M. Zlatic,F.A. Hamprecht<br>
ISBI 2013.Proceedings, (2013), 656-659
</li>
</ul>
</dd>
<dt>Other</dt>
<dd>
<ul>
<li><em>Visualizing a homogeneous blend in bulk heterojunction polymer solar cells by
analytical electron microscopy</em><br>
M. Pfannmöller, H. Flügge, G. Benner, I. Wacker, C. Sommer, M. Hanselmann, S. Schmale, <br>
H. Schmidt, F. A. Hamprecht, T. Rabe, W. Kowalsky, R. Schröder<br>
Nano Letters, (2011) 11, 3099-3107
</li>
</ul>
</dd>
</dt>
</dl>
</p>
</div>
</div>
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