Publications that use and cite TrakEM2

Whitson, Ashley and {Smith III}, Julian P S and Litvaitis, Marian K. 2011. Lehardyia alleithoros, sp. nov. (Turbellaria, Kalyptorhynchia) from the Coast of North Carolina, USA. Southeastern Naturalist 2:221-32. Link.
Anna Kreshuk, Cristoph N. Straehle, Christoph Sommer, Ullrich Koethe, Marco Cantoni, Graham Knott, Fred A. Hamprecht. 2011. Automated Detection and Segmentation of Synaptic Contacts in Nearly Isotropic Serial Electron Microscopy Images. PLoS ONE 6(10): e24899. doi:10.1371/journal.pone.0024899. Link.
Simon Sprecher, Albert Cardona and Volker Hartenstein. 2011. The Drosophila larval visual system: High-resolution analysis of a simple visual neuropil. Developmental Biology 358(1):33-43. Link.
Leena Silvoster M. and Govindan V.K. 2011. Convolutional Neural Network Based Segmentation. Computer Networks and Intelligent Computing: 5th International Conference on Information Processing, ICIP 2011. Link.
Stephan Gerhard, Alessandro Daducci, Alia Lemkaddem, Reto Meuli, Jean-Philippe Thiran, and Patric Hagmann. 2011. The Connectome Viewer Toolkit: An Open Source Framework to Manage, Analyze, and Visualize Connectomes. Frontiers in Neuroinformatics 5:3. Link
Federico Luzzati, Aldo Fasolo and Paolo Peretto. 2011. Combining confocal laser scanning microscopy with serial section reconstruction in the study of adult neurogenesis. Frontiers in Neuroscience 5:0. Link
Huei-Fang Yang and Yoonsuck Choe. 2011. Ground Truth Estimation by Maximizing Topological Agreements in Electron Microscopy Data. Advances in visual computing. Lecture Nodes in Computer Science 6938:371-380. Link.
Yoshiyuki Kubota, Fuyuki Karube, Masaki Nomura, Allan T. Gulledge, Atsushi Mochizuki, Andreas Schertel and Yasuo Kawaguchi. 2011. Conserved properties of dendritic trees in four cortical interneuron subtypes. Scientific Reports 1:89. Link
Martin O'Reilly, Arnd Roth, Michael Häusser and Lewis D. Griffin. 2011. A circle-based method for detection of neural fibre cross-sections in classically stained 2D electron micrographs. MIAAB 2011. Link
F Barron, C Woods, K Kuhn, J Bishop, MJ Howard and DE Clouthier. 2011. Downregulation of Dlx5 and Dlx6 expression by Hand2 is essential for initiation of tongue morphogenesis. Development 138:2249--59. Link.
DD Bock, WC Lee, AM Kerlin, ML Andermann, G Hood, AW Wetzel, S Yurgenson, ER Soucy, HS Kim and RC Reid. 2011. Network anatomy and in vivo physiology of visual cortical neurons. Nature 47(7337):177--82. Link.
N.M. da Costa and K.A.C. Martin. 2011. How thalamus connects to spiny stellate cells in the cat's visual cortex. Journal of Neuroscience 31(8):2925-37. Link.
A. Kreshuk, C.N. Straehle, C. Sommer, U. Koethe, G. Knott and F.A. Hamprecht. 2011. Automated segmentation of synapses in 3D EM data. In: Eighth IEEE International Symposium on Biomedical Imaging (ISBI 2011). Link and PDF.
Lu J. 2011. Neuronal tracing for connectomic studies. Neuroinformatics. DOI:10.1007/s12021-011-9101-6. Link.
Grigorian M, Mandal L, Hakimi M, Ortiz I and Hartenstein V. 2011. The convergence of Notch and MAPK signaling specifies the blood progenitor fate in the Drosophila mesoderm. Developmental Biology 353(1):105-18.
A Cardona, S Saalfeld, S Preibisch, B Schmid, A Cheng, J Pulokas, P Tomancak and V Hartenstein. 2010. An integreated micro- and macroarchitectural analysis of the Drosophila brain by computer-assisted serial section electron microscopy. PLoS Biology 8(10):e100050. Link and PDF.
V. Jain, H.S. Seung and C.T. Turaga. 2010. Machines that learn to segment images: a crucial technology for connectomics. Current Opinion in Neurobiology 20(5):653-66.
D.B. Chklovskii, S. Vitaladevuni and L.K. Scheffer. 2010. Semi-automated reconstruction of neural circuits using electron microscopy. Current Opinion in Neurobiology 20(5):667-75.
A Cardona, S Saalfeld, I Arganda Carreras, W Pereanu, J Schindelin and V Hartenstein. 2010. Identifying neuronal lineages of Drosophila by sequence analysis of axon tracts. Journal of Neuroscience 30(22):7538-53. Link.
P.A. Wieringa, R.W.F.Wiertz, E.L. de Weerd and W.L.C. Rutten. 2010. In vitro Verification of a 3-D Regenerative Neural Interface Design: Examination of Neurite Growth and Electrical Properties Within a Bifurcating Microchannel Structure. Proceedings of the IEEE 98(3):390-7. and PDF.
B. Amandine, A. Cardona, P. Martinez and V. Hartenstein. Structure of the central nervous system of a juvenile acoel, Symsagittifera roscoffensis. 2010. Development Genes and Evolution 220(3):61-76.Link and PDF
V. Kaynig, T. Fuchs and J.M. Buhmann. 2010. Geometrical consistent 3D tracing of neuronal processes in ssTEM data. Medical Image Computing and Computer-Assisted Intervention (MICAI) 6362:209-16.
V. Kaynig, T. Fuchs and J.M. Buhmann. 2010. Neuron geometry extraction by perceptual grouping in ssTEM images. IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR):2902--9.
Huei-Fang Yang and Yoonsuck Choe. 2010. Electron Microscopy Image Segmentation with Graph Cuts Utilizing Estimated Symmetric Three-dimensional Shape Prior. Proceedings of the 6th international conference on Advances in visual computing - Volume Part II. Link, PDF
M.J. Barbera, I. Ruiz-Trillo, J.Y.A. Tufts, A. Bery, J.D. Silberman and A.J. Roger. 2010. Sawyeria marylandensis (Heterolobosea) has a hydrogenosome with novel metabolic properties. Eucaryotic Cell 9:(12):1913-24.

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