Neuronize v2: Bridging the Gap Between Existing Proprietary Tools to Optimize Neuroscientific Workflows

Knowledge about neuron morphology is key to understanding brain structure and function. There are a variety of software tools that are used to segment and trace the neuron morphology. However, these tools usually utilize proprietary formats. This causes interoperability problems since the information extracted with one tool cannot be used in other tools. This article aims to improve neuronal reconstruction workflows by facilitating the interoperability between two of the most commonly used software tools—Neurolucida (NL) and Imaris (Filament Tracer). The new functionality has been included in an existing tool—Neuronize—giving rise to its second version. Neuronize v2 makes it possible to automatically use the data extracted with Imaris Filament Tracer to generate a tracing with dendritic spine information that can be read directly by NL. It also includes some other new features, such as the ability to unify and/or correct inaccurately-formed meshes (i.e., dendritic spines) and to calculate new metrics. This tool greatly facilitates the process of neuronal reconstruction, bridging the gap between existing proprietary tools to optimize neuroscientific workflows.This work was supported by grants from the following entities: the Spanish ‘‘Ministerio de Ciencia, Innovación y Universidades’’ regarding grant TIN2017-83132-C2 (corresponding to the project ‘‘Analytical Applied Visualization,’’ VIANA), grant PGC2018-094307-B-I00, the Cajal Blue Brain Project [the Spanish partner of the Blue Brain Project initiative from L’Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland]; and the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the specific grant agreement No. 785907 (Human Brain Project SGA2) and the specific grant agreement No. 945539 (Human Brain Project SGA3)