Computational Neuroanatomy Plugin Integration

The BrainGlobe Initiative was created to develop open-source tools and standards for computational neuroanatomy in Python. This team will further those efforts and provide an integrated workflow for whole-brain microscopy analyses within napari. This project will ensure full compatibility between existing BrainGlobe plugins. In particular, this functionality will allow the user to remain in the napari environment without having to save any data to a disk.

All functionality will be available within the graphical user interface, and rely on custom functionality (e.g. data stored outside of napari layers) as little as possible, to ensure maximal compatibility with the napari ecosystem.

The next phase of this work is to develop a BrainGlobe-napari “meta-plugin” to bring all functionality together in a single plugin. This will simplify the use of these tools for whole-brain microscopy analysis workflows, for which many types of analysis may be needed in a single dataset, such as atlas registration, implant segmentation, and mapping of labelled cells. This will also improve the sustainability and interoperability of the BrainGlobe plugins, as the meta-plugin can be used to test the integration of all tools. The group will also work to develop interoperability with other existing napari plugins for additional or complementary analyses, so that napari can be used for all types of analysis, including those not implemented within the BrainGlobe ecosystem.

The analysis of whole-brain microscopy datasets represents an unmet need in neuroscience. While tools are available, a single graphical analysis package that can easily integrate with the growing Python-based image analysis community does not yet exist. This integration effort may significantly increase access for researchers to perform their entire image analysis pipeline in napari. The team aims to catalyze the development of further analysis tools as napari plugins, particularly for the analysis of other whole-organ datasets.