publications.html

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title: Publications
category: "Publications"
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    <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://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>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>
        <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>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>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>Exploring the third dimension: Volume electron microscopy comes of age</em><br>
        C.J. Peddie, L.M. Collinson<br>
        Micron, 2014
        </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=http://scholar.google.com/scholar?start=40&hl=en&as_sdt=0,5&sciodt=0,5&cites=8459688359110226056&scipsc=>
      google scholar</a> for the full listing.
      <ul>
        <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>
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