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Neuron Reconstruction Algorithms
Right now 53 implementations/variants of 31 methods (tracing algorithms) have been ported to BigNeuron. Excluding 8 variants that use machine learning to improve the performance of several algorithms and one method that is too slow to be tested, there are 44 implementations (called "algorithms" hereafter) used in bench testing for most of the BigNeuron image data.
All of the neuron tracing software can be downloaded from the latest binary release of Vaa3D. Please check the Vaa3D Github project page for more information (the source code locations are documented below as well). Once you launch the software, the tracing methods are available in from the "main menu -> Plugins -> Neuron Tracing menu". These methods can be executed from either GUI or command line. Due to the limitation of such dependency libraries for various tracing algorithms, the most complete set of tracing methods are available for Linux at this moment.
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/neurontracing_vn2
Output reconstruction suffix: *_app2.swc
Special library dependency: NO
Available for platforms: Windows, Mac, and Linux
Publication(s): Xiao, H. and Peng, H. (2013) APP2: automatic tracing of 3D neuron morphology based on hierarchical pruning of a gray-weighted image distance-tree, Bioinformatics, 29, 1448-1454. (http://home.penglab.com/papersall/docpdf/2013_BIOINFO_app2.pdf)
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/neurontracing_vn2
Output reconstruction suffix: *_app1.swc
Special library dependency: NO
Available for platforms: Windows, Mac, and Linux
Publication(s): Peng, H., Long, F. and Myers, G. (2011) Automatic 3D neuron tracing using all-path pruning, Bioinformatics, 27, i239-i247. (http://home.penglab.com/papersall/docpdf/2011_Bioinfo_ISMB_allpathpruning.pdf)
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/bigneuron_miroslav_r_Advantra
Output reconstruction suffix: *_Advantra.swc
Special library dependency: NO
Available for platforms: Windows, Mac, and Linux
Publication(s): NA
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/bigneuron_jiezhou_recon_3d_thin_v1
Output reconstruction suffix: *_axis_analyzer.swc
Special library dependency: NO
Available for platforms: Windows, Mac, and Linux
Publication(s): NA
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/bigneuron_zhijiang_zn_bjut_fastmarching_spanningtree_vaa3d
Output reconstruction suffix: *_fastmarching_spanningtree.swc
Special library dependency: NO
Available for platforms: Windows, Mac, and Linux
Publication(s): NA
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/bigneuron_zhijiang_zn_bjut_MeanshiftSpanningtree
Output reconstruction suffix: *_meanshift.swc
Special library dependency: NO
Available for platforms: Windows, Mac, and Linux
Publication(s): NA
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/bigneuron_chingwei_ENT
Output reconstruction suffix: *_ENT.swc
Special library dependency: NO
Available for platforms: Windows, Mac, and Linux
Publication(s): NA
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/bigneuron_AmosSironi_PrzemyslawGlowacki_RegMST_tracing_plugin
Output reconstruction suffix: *_tubularity_model_S.v3draw_MST_Tracing_Ws_21_th_170.swc
Special library dependency: NO
Available for platforms: Windows, Mac, and Linux
Publication(s): NA
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/bigneuron_zz_snake_tracing
Output reconstruction suffix: *_snake.swc
Special library dependency: ITK static library
Available for platforms: Mac, and Linux
Comments: Follow the instruction in the README file
Publication(s): Narayanaswamy, A., Wang, Y., & Roysam, B. (2011). 3-D image pre-processing algorithms for improved automated tracing of neuronal arbors. Neuroinformatics, 9(2-3): 219-231. (http://link.springer.com/article/10.1007%2Fs12021-011-9116-z)
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/bigneuron_LinGU_LCM_boost
Output reconstruction suffix: *_LCMboost.swc
Special library dependency: Need shared libraies under /vaa3d_tools/bigneuron_ported/LinGU/LCM_boost/lib_centos, including libopencv_core.so, libopencv_core.so.3.0.0, libopencv_imgproc.so.3.0, libopencv_ml.so, libopencv_ml.so.3.0.0, libopencv_core.so.3.0, libopencv_imgproc.so, libopencv_imgproc.so.3.0.0, libopencv_ml.so.3.0
Available for platforms: Linux
Publication(s): (under review)
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/neurontracing_MOST
Output reconstruction suffix: *_MOST.swc
Special library dependency: NO
Available for platforms: Windows, Mac, and Linux
Publication(s): Wu, J., et al. (2014) 3D BrainCV: Simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution, NeuroImage, 87, 199-208. (http://www.sciencedirect.com/science/article/pii/S1053811913010598)
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/bigneuron_zz_neurontracing_mst
Output reconstruction suffix: *_MST_Tracing.swc
Special library dependency: NO
Available for platforms: Mac, and Linux
Publication(s): NA
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/bigneuron_ytc_nctuTW
Output reconstruction suffix: *_nctuTW.swc
Special library dependency: NO
Available for platforms: Mac, and Linux
Publication(s): Lee, P. C., Chuang, C. C., Chiang, A. S., & Ching, Y. T. (2012). High-throughput computer method for 3d neuronal structure reconstruction from the image stack of the Drosophila brain and its applications. PLoS Comput Biol, 8(9), e1002658. (http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002658)
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/bigneuron_ytc_zz_nctuTW_tips
Output reconstruction suffix: *_nctuTW_GD.swc
Special library dependency: NO
Available for platforms: Mac, and Linux
Publication(s): NA
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/bigneuron_miroslav_r_NeuronChaser
Output reconstruction suffix: *_NeuronChaser.swc
Special library dependency: NO
Available for platforms: Linux
Publication(s): NA
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/bigneuron_zhouhang_hust_NeuroGPSTree
Output reconstruction suffix: *_NeuroGPSTree.swc
Special library dependency: NO
Available for platforms: Mac, and Linux
Publication(s): Quan, T., Zhou, H., Li, J., Li, S., Li, A., Li, Y., ... & Zeng, S. (2016). NeuroGPS-Tree: automatic reconstruction of large-scale neuronal populations with dense neurites. Nature methods, 13(1), 51-54. (http://www.nature.com/nmeth/journal/v13/n1/abs/nmeth.3662.html)
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/bigneuron_siqi_stalker_v3d
Output reconstruction suffix: *_NeuroStalker.swc
Special library dependency: ITK static library
Available for platforms: Mac, and Linux
Publication(s): NA
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/bigneuron_ting_dezhe_neutu_autotrace
Output reconstruction suffix: *_neutu_autotrace.swc
Special library dependency: NO
Available for platforms: Mac, and Linux
Publication(s): NA
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/bigneuron_ting_neutube
Output reconstruction suffix: *_neutube.swc
Special library dependency: Need shared libraies: /v3d_external/v3d_main/common_lib/lib/libneurolabi_debug.so, /vaa3d_tools/released_plugins/v3d_plugins/neurontracing_neutube/src_neutube/neurolabi/lib/fftw3/lib/libfftw3f.so, /vaa3d_tools/released_plugins/v3d_plugins/neurontracing_neutube/src_neutube/neurolabi/lib/fftw3/lib/libfftw3.so, /vaa3d_tools/released_plugins/v3d_plugins/neurontracing_neutube/src_neutube/neurolabi/lib/xml/lib/libxml2.so
Available for platforms: Mac, and Linux
Publication(s): Zhao, T., Xie, J., Amat, F., Clack, N., Ahammad, P., Peng, H., Long, F., & Myers, E. (2011). Automated reconstruction of neuronal morphology based on local geometrical and global structural models. Neuroinformatics, 9(2-3): 247-261. (http://link.springer.com/article/10.1007%2Fs12021-011-9120-3)
Comment: Follow the instruction in the README file
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/bigneuron_chingwei_EnsembleNeuronTracerBasic
Output reconstruction suffix: *_EnsembleNeuronTracerBasic.swc
Special library dependency: NO
Available for platforms: Windows, Mac, and Linux
Publication(s): NA
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/bigneuron_chingwei_CWlab_method1_version1
Output reconstruction suffix: *_Cwlab_ver1.swc
Special library dependency: NO
Available for platforms: Mac, and Linux
Publication(s): NA
Source code location: /vaa3d_tools/bigneuron_ported/chingwei/EnsembleNeuronTracerV2n
Output reconstruction suffix: *_EnsembleNeuronTracerV2n.swc
Special library dependency: NO
Available for platforms: Windows, Mac, and Linux
Publication(s): NA
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/bigneuron_chingwei_EnsembleNeuronTracerV2n
Output reconstruction suffix: *_EnsembleNeuronTracerV2s.swc
Special library dependency: NO
Available for platforms: Windows, Mac, and Linux
Publication(s): NA
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/bigneuron_zz_PSF_tracing
Output reconstruction suffix: NA
Special library dependency: NO
Available for platforms: Currently unavailable for release due to extremely slow running speed.
Publication(s): Bas, E., & Erdogmus, D. (2011). Principal curves as skeletons of tubular objects: locally characterizing the structures of axons. Neuroinformatics, 9(2-3): 181-191. (http://link.springer.com/article/10.1007%2Fs12021-011-9105-2)
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/bigneuron_pengyu_zhihao_3DTraceSWC
Output reconstruction suffix: *_pyzh.swc
Special library dependency: Needs MCR (Matlab Compiler Runtime)
Available for platforms: Windows, Mac, and Linux
Publication(s): NA
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/bigneuron_siqi_rivuletv3d
Output reconstruction suffix: *_Rivulet.swc
Special library dependency: NO
Available for platforms: Linux
Publication(s): Liu, S. (2016) ISBI'2016. (in press)
Comments: On CentOS, it needs gcc 4.8.x to build
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/neurontracing_simpletracing
Output reconstruction suffix: *_simple.swc
Special library dependency: NO
Available for platforms: Windows, Mac, and Linux
Publication(s): Yang, J., Gonzalez-Bellido, P.T. and Peng, H. (2013) A distance-field based automatic neuron tracing method, BMC bioinformatics, 14, 93. (http://link.springer.com/article/10.1186%2F1471-2105-14-93)
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/neurontracing_simpletracing
Output reconstruction suffix: *_Rollerball.swc
Special library dependency: NO
Available for platforms: Windows, Mac, and Linux
Publication(s): Yang, J., Gonzalez-Bellido, P.T. and Peng, H. (2013) A distance-field based automatic neuron tracing method, BMC bioinformatics, 14, 93. (http://link.springer.com/article/10.1186%2F1471-2105-14-93)
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/neurontracing_simpletracing
Output reconstruction suffix: *_Rayshooting.swc
Special library dependency: NO
Available for platforms: Windows, Mac, and Linux
Publication(s): Yang, J., Gonzalez-Bellido, P.T. and Peng, H. (2013) A distance-field based automatic neuron tracing method, BMC bioinformatics, 14, 93. (http://link.springer.com/article/10.1186%2F1471-2105-14-93)
Source code location: /vaa3d_tools/hackathon/hanbo/neurontracing_selfCorrect
Output reconstruction suffix: *_smartTracing.swc
Special library dependency: NO
Available for platforms: Windows, Mac, and Linux
Publication(s): Chen, H., Xiao, H., Liu, T., & Peng, H. (2015). SmartTracing: self-learning-based neuron reconstruction. Brain Informatics, 2(3), 135-144. (http://link.springer.com/article/10.1007%2Fs40708-015-0018-y)
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/bigneuron_zz_neurontracing_TReMAP
Output reconstruction suffix: *_XY_3D_TreMap.swc
Special library dependency: NO
Available for platforms: Windows, Mac, and Linux
Publication(s): Zhou, Z., Liu, X., Long, B., & Peng, H. (2016). TReMAP: Automatic 3D neuron reconstruction based on tracing, reverse mapping and assembling of 2D projections. Neuroinformatics, 14(1), 41-50. (http://home.penglab.com/papersall/docpdf/2015_Neuroinfo_TReMAP.pdf)
Source code location: /vaa3d_tools/released_plugins/v3d_plugins/bigneuron_hide_ikeno_SIGEN
Output reconstruction suffix: *_SIGEN.swc
Special library dependency: NO
Available for platforms: Linux
Publication(s): NA