Blik is an extensible 3D visualisation tool for the annotation and analysis of cryo-electron tomography data

Lorenzo Gaifas, Moritz A Kirchner, Joanna Timmins and Irina Gutsche

PLOS Biology, 2024, vol. 22, issue 4, 1-18

Abstract: Powerful, workflow-agnostic and interactive visualisation is essential for the ad hoc, human-in-the-loop workflows typical of cryo-electron tomography (cryo-ET). While several tools exist for visualisation and annotation of cryo-ET data, they are often integrated as part of monolithic processing pipelines, or focused on a specific task and offering limited reusability and extensibility. With each software suite presenting its own pros and cons and tools tailored to address specific challenges, seamless integration between available pipelines is often a difficult task. As part of the effort to enable such flexibility and move the software ecosystem towards a more collaborative and modular approach, we developed blik, an open-source napari plugin for visualisation and annotation of cryo-ET data (source code: https://github.com/brisvag/blik). blik offers fast, interactive, and user-friendly 3D visualisation thanks to napari, and is built with extensibility and modularity at the core. Data is handled and exposed through well-established scientific Python libraries such as numpy arrays and pandas dataframes. Reusable components (such as data structures, file read/write, and annotation tools) are developed as independent Python libraries to encourage reuse and community contribution. By easily integrating with established image analysis tools—even outside of the cryo-ET world—blik provides a versatile platform for interacting with cryo-ET data. On top of core visualisation features—interactive and simultaneous visualisation of tomograms, particle picks, and segmentations—blik provides an interface for interactive tools such as manual, surface-based and filament-based particle picking, and image segmentation, as well as simple filtering tools. Additional self-contained napari plugins developed as part of this work also implement interactive plotting and selection based on particle features, and label interpolation for easier segmentation. Finally, we highlight the differences with existing software and showcase blik’s applicability in biological research.A common challenge encountered by researchers working on cryo-ET data is the incompatibility between different software tools. This study develops a napari-based 3D visualization and analysis tool, named blik, that is compatible with commonly used cryo-ET processing packages.

Date: 2024
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DOI: 10.1371/journal.pbio.3002447

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