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Development of MethodsJ2 for napari Plugins

Award napari Plugin Accelerator

Project Summary

Methods reporting in bioimaging are often incomplete, making it impossible to replicate key studies. Recent efforts to standardize metadata reporting for bioimaging and develop tools to help researchers collect and report critical information required for reproducibility of bioimaging experiments include the MethodsJ2 software tool, which has a visually intuitive graphical interface and is designed to facilitate the collection of microscope hardware/software specifications metadata and image acquisition settings that are stored in a Microscope.JSON file.

MethodsJ2 is a script written in Python and implemented in ImageJ/Fiji, which helps improve imaging methods reporting by assisting with writing methods sections that are accurate and complete. This project proposes to adapt MethodsJ2 and implement it in the napari ecosystem as a plugin called napari-methods.

Group collaboration will be crucial to introducing this plugin and encouraging uptake. The team will solicit participation in a hackathon to guide the definition of a roadmap towards the refinement and development of napari-methods-v2.0. Detailed training videos and a workshop will be developed to launch napari-methods-v2.0, and a manuscript will be published on bioRxiv and sent to a journal for review and publication. The group will conduct outreach to imaging scientists and offer training for those interested in bringing the tool back to their imaging facility users for plugin dissemination. These training sessions and an international workshop will gather a diverse audience to invite more imaging scientists to use the plugin. The project will encourage methods reporting as a standard practice and further develop napari’s plugin resources.


Principal Investigator
Claire Brown, PhD
Claire Brown, PhD
Co-Principal Investigator
Caterina Strambio-De-Castillia, PhD
Caterina Strambio-De-Castillia, PhD