neuTube 1.0: A New Design for Efficient Neuron Reconstruction Software Based on the SWC Format 123
نویسندگان
چکیده
Brain circuit mapping requires digital reconstruction of neuronal morphologies in complicated networks. Despite recent advances in automatic algorithms, reconstruction of neuronal structures is still a bottleneck in circuit mapping due to a lack of appropriate software for both efficient reconstruction and user-friendly editing. Here we present a new software design based on the SWC format, a standardized neuromorphometric format that has been widely used for analyzing neuronal morphologies or sharing neuron reconstructions via online archives such as NeuroMorpho.org. We have also implemented the design in our open-source software called neuTube 1.0. As specified by the design, the software is equipped with parallel 2D and 3D visualization and intuitive neuron tracing/editing functions, allowing the user to efficiently reconstruct neurons from fluorescence image data and edit standard neuron structure files produced by any other reconstruction software. We show the advantages of neuTube 1.0 by comparing it to two other software tools, namely Neuromantic and Neurostudio. The software is available for free at http://www.neutracing.com, which also hosts complete software documentation and video tutorials.
منابع مشابه
neuTube 1.0: A New Design for Efficient Neuron Reconstruction Software Based on the SWC Format.
Brain circuit mapping requires digital reconstruction of neuronal morphologies in complicated networks. Despite recent advances in automatic algorithms, reconstruction of neuronal structures is still a bottleneck in circuit mapping due to a lack of appropriate software for both efficient reconstruction and user-friendly editing. Here we present a new software design based on the SWC format, a s...
متن کاملReconstruction of the neural network model of motor control for virtual C.elegans on the basis of actual organism information
Introduction: C. elegans neural network is a good sample for neural networks studies, because its structural details are completely determined. In this study, the virtual neural network of this worm that was proposed by Suzuki et al. for control of movement was reconstructed by adding newly discovered synapses for each of these network neurons. These synapses are newly discovered in the actu...
متن کاملDesign and implementation of multi-signal and time-varying neural reconstructions
Several efficient procedures exist to digitally trace neuronal structure from light microscopy, and mature community resources have emerged to store, share, and analyze these datasets. In contrast, the quantification of intracellular distributions and morphological dynamics is not yet standardized. Current widespread descriptions of neuron morphology are static and inadequate for subcellular ch...
متن کاملA New Optimized Hybrid Model Based On COCOMO to Increase the Accuracy of Software Cost Estimation
The literature review shows software development projects often neither meet time deadlines, nor run within the allocated budgets. One common reason can be the inaccurate cost estimation process, although several approaches have been proposed in this field. Recent research studies suggest that in order to increase the accuracy of this process, estimation models have to be revised. The Construct...
متن کاملA New Fast and Efficient HMM-Based Face Recognition System Using a 7-State HMM Along With SVD Coefficients
In this paper, a new Hidden Markov Model (HMM)-based face recognition system is proposed. As a novel point despite of five-state HMM used in pervious researches, we used 7-state HMM to cover more details. Indeed we add two new face regions, eyebrows and chin, to the model. As another novel point, we used a small number of quantized Singular Values Decomposition (SVD) coefficients as feature...
متن کامل