NeuroEditor: a tool to edit and visualize neuronal morphologies
The digital extraction of detailed neuronal morphologies from microscopy data is an essential step in the study of neurons. Ever since Cajal’s work, the acquisition and analysis of neuron anatomy has yielded invaluable insight into the nervous system, which has led to our present understanding of ma...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2024-02-01
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| Series: | Frontiers in Neuroanatomy |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fnana.2024.1342762/full |
| _version_ | 1811153629187407872 |
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| author | Ivan Velasco Juan J. Garcia-Cantero Juan J. Garcia-Cantero Juan P. Brito Juan P. Brito Sofia Bayona Sofia Bayona Luis Pastor Luis Pastor Susana Mata Susana Mata |
| author_facet | Ivan Velasco Juan J. Garcia-Cantero Juan J. Garcia-Cantero Juan P. Brito Juan P. Brito Sofia Bayona Sofia Bayona Luis Pastor Luis Pastor Susana Mata Susana Mata |
| author_sort | Ivan Velasco |
| collection | DOAJ |
| description | The digital extraction of detailed neuronal morphologies from microscopy data is an essential step in the study of neurons. Ever since Cajal’s work, the acquisition and analysis of neuron anatomy has yielded invaluable insight into the nervous system, which has led to our present understanding of many structural and functional aspects of the brain and the nervous system, well beyond the anatomical perspective. Obtaining detailed anatomical data, though, is not a simple task. Despite recent progress, acquiring neuron details still involves using labor-intensive, error prone methods that facilitate the introduction of inaccuracies and mistakes. In consequence, getting reliable morphological tracings usually needs the completion of post-processing steps that require user intervention to ensure the extracted data accuracy. Within this framework, this paper presents NeuroEditor, a new software tool for visualization, editing and correction of previously reconstructed neuronal tracings. This tool has been developed specifically for alleviating the burden associated with the acquisition of detailed morphologies. NeuroEditor offers a set of algorithms that can automatically detect the presence of potential errors in tracings. The tool facilitates users to explore an error with a simple mouse click so that it can be corrected manually or, where applicable, automatically. In some cases, this tool can also propose a set of actions to automatically correct a particular type of error. Additionally, this tool allows users to visualize and compare the original and modified tracings, also providing a 3D mesh that approximates the neuronal membrane. The approximation of this mesh is computed and recomputed on-the-fly, reflecting any instantaneous changes during the tracing process. Moreover, NeuroEditor can be easily extended by users, who can program their own algorithms in Python and run them within the tool. Last, this paper includes an example showing how users can easily define a customized workflow by applying a sequence of editing operations. The edited morphology can then be stored, together with the corresponding 3D mesh that approximates the neuronal membrane. |
| first_indexed | 2024-03-08T02:02:31Z |
| format | Article |
| id | doaj.art-2d8fd89686cf4af49ea6e33ed4d8e373 |
| institution | Directory Open Access Journal |
| issn | 1662-5129 |
| language | English |
| last_indexed | 2024-03-08T02:02:31Z |
| publishDate | 2024-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Neuroanatomy |
| spelling | doaj.art-2d8fd89686cf4af49ea6e33ed4d8e3732024-02-14T04:16:31ZengFrontiers Media S.A.Frontiers in Neuroanatomy1662-51292024-02-011810.3389/fnana.2024.13427621342762NeuroEditor: a tool to edit and visualize neuronal morphologiesIvan Velasco0Juan J. Garcia-Cantero1Juan J. Garcia-Cantero2Juan P. Brito3Juan P. Brito4Sofia Bayona5Sofia Bayona6Luis Pastor7Luis Pastor8Susana Mata9Susana Mata10Department of Computer Science, Universidad Rey Juan Carlos (URJC), Tulipan, Madrid, SpainDepartment of Computer Science, Universidad Rey Juan Carlos (URJC), Tulipan, Madrid, SpainCenter for Computational Simulation, Universidad Politecnica de Madrid, Madrid, SpainCenter for Computational Simulation, Universidad Politecnica de Madrid, Madrid, SpainDLSIIS, ETSIINF, Universidad Politecnica de Madrid, Madrid, SpainDepartment of Computer Science, Universidad Rey Juan Carlos (URJC), Tulipan, Madrid, SpainCenter for Computational Simulation, Universidad Politecnica de Madrid, Madrid, SpainDepartment of Computer Science, Universidad Rey Juan Carlos (URJC), Tulipan, Madrid, SpainCenter for Computational Simulation, Universidad Politecnica de Madrid, Madrid, SpainDepartment of Computer Science, Universidad Rey Juan Carlos (URJC), Tulipan, Madrid, SpainCenter for Computational Simulation, Universidad Politecnica de Madrid, Madrid, SpainThe digital extraction of detailed neuronal morphologies from microscopy data is an essential step in the study of neurons. Ever since Cajal’s work, the acquisition and analysis of neuron anatomy has yielded invaluable insight into the nervous system, which has led to our present understanding of many structural and functional aspects of the brain and the nervous system, well beyond the anatomical perspective. Obtaining detailed anatomical data, though, is not a simple task. Despite recent progress, acquiring neuron details still involves using labor-intensive, error prone methods that facilitate the introduction of inaccuracies and mistakes. In consequence, getting reliable morphological tracings usually needs the completion of post-processing steps that require user intervention to ensure the extracted data accuracy. Within this framework, this paper presents NeuroEditor, a new software tool for visualization, editing and correction of previously reconstructed neuronal tracings. This tool has been developed specifically for alleviating the burden associated with the acquisition of detailed morphologies. NeuroEditor offers a set of algorithms that can automatically detect the presence of potential errors in tracings. The tool facilitates users to explore an error with a simple mouse click so that it can be corrected manually or, where applicable, automatically. In some cases, this tool can also propose a set of actions to automatically correct a particular type of error. Additionally, this tool allows users to visualize and compare the original and modified tracings, also providing a 3D mesh that approximates the neuronal membrane. The approximation of this mesh is computed and recomputed on-the-fly, reflecting any instantaneous changes during the tracing process. Moreover, NeuroEditor can be easily extended by users, who can program their own algorithms in Python and run them within the tool. Last, this paper includes an example showing how users can easily define a customized workflow by applying a sequence of editing operations. The edited morphology can then be stored, together with the corresponding 3D mesh that approximates the neuronal membrane.https://www.frontiersin.org/articles/10.3389/fnana.2024.1342762/fullvisualizationneuron morphologytracingneuron editingcorrectionmesh |
| spellingShingle | Ivan Velasco Juan J. Garcia-Cantero Juan J. Garcia-Cantero Juan P. Brito Juan P. Brito Sofia Bayona Sofia Bayona Luis Pastor Luis Pastor Susana Mata Susana Mata NeuroEditor: a tool to edit and visualize neuronal morphologies Frontiers in Neuroanatomy visualization neuron morphology tracing neuron editing correction mesh |
| title | NeuroEditor: a tool to edit and visualize neuronal morphologies |
| title_full | NeuroEditor: a tool to edit and visualize neuronal morphologies |
| title_fullStr | NeuroEditor: a tool to edit and visualize neuronal morphologies |
| title_full_unstemmed | NeuroEditor: a tool to edit and visualize neuronal morphologies |
| title_short | NeuroEditor: a tool to edit and visualize neuronal morphologies |
| title_sort | neuroeditor a tool to edit and visualize neuronal morphologies |
| topic | visualization neuron morphology tracing neuron editing correction mesh |
| url | https://www.frontiersin.org/articles/10.3389/fnana.2024.1342762/full |
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