The Filament Editor: An Interactive Software Environment for Visualization, Proof-Editing and Analysis of 3D Neuron Morphology
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Neuroanatomical analysis, such as classification of cell types, depends on reliable reconstruction of large numbers of complete 3D dendrite and axon morphologies. At present, the majority of neuron reconstructions are obtained from preparations in a single tissue slice in vitro, thus suffering from cut off dendrites and, more dramatically, cut off axons. In general, axons can innervate volumes of several cubic millimeters and may reach path lengths of tens of centimeters. Thus, their complete reconstruction requires in vivo labeling, histological sectioning and imaging of large fields of view. Unfortunately, anisotropic background conditions across such large tissue volumes, as well as faintly labeled thin neurites, result in incomplete or erroneous automated tracings and even lead experts to make annotation errors during manual reconstructions. Consequently, tracing reliability renders the major bottleneck for reconstructing complete 3D neuron morphologies. Here, we present a novel set of tools, integrated into a software environment named ‘Filament Editor’, for creating reliable neuron tracings from sparsely labeled in vivo datasets. The Filament Editor allows for simultaneous visualization of complex neuronal tracings and image data in a 3D viewer, proof-editing of neuronal tracings, alignment and interconnection across sections, and morphometric analysis in relation to 3D anatomical reference structures. We illustrate the functionality of the Filament Editor on the example of in vivo labeled axons and demonstrate that for the exemplary dataset the final tracing results after proof-editing are independent of the expertise of the human operator.
KeywordsAutomated neuron tracing Axon Dendrite Alignment of brain sections Barrel cortex
We thank Bert Sakmann and Philip J. Broser for advice and assistance during early stages of the project; Wolfgang Holler and Britta Weber for their contribution to the Filament Editor; Marianne Krabi and Jonas Hörsch for assisting with the analysis functionality; Norbert Lindow for providing the LineRayCaster. Randy M. Bruno and Christiaan P.J. de Kock for supplying biocytin-labeled neurons; Lothar Baltruschat, Richard Smith, Kevin Pels, and Ariel Lee for proof-editing; Hans-Joachim Wagner and the entire staff of the Anatomy Institute of the University of Tuebingen for their generous support. Funding was provided by the Bernstein Center for Computational Neuroscience, Tuebingen (funded by the German Federal Ministry of Education and Research (BMBF; FKZ: 01GQ1002)) (MO), by the Max Planck Institute for Biological Cybernetics, Tuebingen (MO), by the Max Planck Florida Institute for Neuroscience, Jupiter (MO), by the Werner Reichardt Center for Integrative Neuroscience, Tuebingen (MO), by the Zuse Institute Berlin (VJD, HCH) and the Max Planck Institute of Neurobiology, Martinsried (VJD). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Conceived and designed the project: MO. Developed the Filament Editor and associated functionalities: VJD. Analyzed the data and wrote the paper: VJD, HCH, MO.
- Broser, P. J., Grinevich, V., Osten, P., Sakmann, B., & Wallace, D. J. (2008). Critical period plasticity of axonal arbors of layer 2/3 pyramidal neurons in rat somatosensory cortex: layer-specific reduction of projections into deprived cortical columns. Cerebral Cortex, 18(7), 1588–1603.PubMedCentralPubMedCrossRefGoogle Scholar
- Carnevale, N. T., & Hines, M. L. (2006). The NEURON Book: University Press.Google Scholar
- Dercksen, V. J., Weber, B., Guenther, D., Oberlaender, M., Prohaska, S., & Hege, H. C. (2009). Automatic alignment of stacks of filament data. IEEE Int. Symp. on Biomedical Imaging: From Nano to Macro (ISBI), 971–974.Google Scholar
- FEI-VisualizationSciencesGroup (2013a). Amira 5.5. www.vsg3d.com/amira/overview
- FEI-VisualizationSciencesGroup (2013b). Amira 5.5 Reference Guide. www.vsg3d.com/sites/default/files/Amira_Reference_Guide.pdf
- Frick, A., Feldmeyer, D., Helmstaedter, M., & Sakmann, B. (2007). Monosynaptic Connections between Pairs of L5A Pyramidal Neurons in Columns of Juvenile Rat Somatosensory Cortex. Cereb Cortex 18(2), 397-406.Google Scholar
- Fuchs, H., Kedem, Z. M., & Uselton, S. P. (1977). Optimal Surface Reconstruction from Planar Contours (Vol. 20, Communications of the ACM, 20(10), 693-702).Google Scholar
- Hill, S. L., Wang, Y., Riachi, I., Schurmann, F., & Markram, H. (2012). Statistical connectivity provides a sufficient foundation for specific functional connectivity in neocortical neural microcircuits. Proceedings of the National Academy of Sciences of the United States of America, 109(42), E2885–E2894. doi: 10.1073/pnas.1202128109.PubMedCentralPubMedCrossRefGoogle Scholar
- Liang, Y. D., Barsky, B. A., & M., S. (1992). Some Improvements to a Parametric Line Clipping Algorithm. Tech. Rep. UCB/CSD-92-688. EECS Department, University of California, Berkley.Google Scholar
- Luisi, J., Narayanaswamy, A., Galbreath, Z., & Roysam, B. (2011). The FARSIGHT trace editor: an open source tool for 3-D inspection and efficient pattern analysis aided editing of automated neuronal reconstructions. Neuroinformatics, 9(2–3), 305–315. doi: 10.1007/s12021-011-9115-0.PubMedCrossRefGoogle Scholar
- Mayerich, D., Bjornsson, C., Taylor, J., & Roysam, B. (2011). Metrics for Comparing Explicit Representations of Interconnected Biological Networks. In IEEE Symposium on Biological Data Visualization, Providence RI, (pp. 79–86).Google Scholar
- Nielsen, J., & Mack, R. L. (1994). Usability Inspection Methods: John Wiley & Sons, Inc.Google Scholar
- Oberlaender, M., Boudewijns, Z. S., Kleele, T., Mansvelder, H. D., Sakmann, B., & de Kock, C. P. (2011). Three-dimensional axon morphologies of individual layer 5 neurons indicate cell type-specific intracortical pathways for whisker motion and touch. Proceedings of the National Academy of Sciences of the United States of America, 108(10), 4188–4193. doi: 10.1073/pnas.1100647108.PubMedCentralPubMedCrossRefGoogle Scholar
- Oberlaender, M., de Kock, C. P. J., Bruno, R. M., Ramirez, A., Meyer, H. S., Dercksen, V. J., et al. (2012a). Cell Type-Specific Three-Dimensional Structure of Thalamocortical Circuits in a Column of Rat Vibrissal Cortex. Cerebral Cortex, 22(10), 2375-2391 (New York, NY : 1991), doi: 10.1093/cercor/bhr317.
- Pinault, D. (1996). A novel single-cell staining procedure performed in vivo under electrophysiological control: morpho-functional features of juxtacellularly labeled thalamic cells and other central neurons with biocytin or Neurobiotin. Journal of Neuroscience Methods, 65(2), 113–136.PubMedCrossRefGoogle Scholar
- Sigg, C., Weyerich, T., Botsch, M., & Gross, M. GPU-Based Ray-Casting of Quadratic Surfaces. In 3rd Eurographics/IEEE VGTC conference on Point-Based Graphics, Boston MA, 2006 (pp. 59–65).Google Scholar
- Skiena, S. (1998). The algorithm design manual: Springer Verlag New York.Google Scholar
- Wearne, S. L., Rodriguez, A., Ehlenberger, D. B., Rocher, A. B., Henderson, S. C., & Hof, P. R. (2005). New techniques for imaging, digitization and analysis of three-dimensional neural morphology on multiple scales. Neuroscience, 136(3), 661–680. doi: 10.1016/j.neuroscience.2005.05.053.PubMedCrossRefGoogle Scholar
- Wills, G. J. (1996). Selection: 524,288 ways to say “this is interesting”. In IEEE Symposium on Information Visualization, (pp. 54–60)Google Scholar