This organization collects the open-source repositories that make up the brim ecosystem — a standardized framework for storing, sharing, and analyzing data from Brillouin light scattering (BLS) microscopy.
Reference publication: Bevilacqua, Hambura, Bouvet et al., "A standardized file format and open-source analysis framework for Brillouin microscopy data" · arXiv:2509.07566
Brillouin microscopy enables label-free, non-contact 3D mapping of the viscoelastic properties of living cells and tissues. As the field grows, the lack of standardized methods for storing and analyzing spectral data has become a critical bottleneck — limiting reproducibility and making cross-lab comparisons difficult.
The brim ecosystem addresses this by providing:
- A standardized file format (
brim) based on Zarr v3, designed for cloud-compatible, hierarchical storage of spectral data, derived maps, and rich acquisition metadata. - Open-source tools for reading, writing, validating, visualizing, and analyzing brim files.
Together, these tools promote FAIR data practices (Findable, Accessible, Interoperable, Reusable) across the Brillouin microscopy community.
| Repository | Description |
|---|---|
| Brillouin-standard-file | Specification and discussion of the brim file format standard |
| brimfile | Python library to read and write brim files, including spectral data, derived maps, and metadata |
| BrimView | Browser-based GUI for visualization and real-time spectral analysis of brim files — no installation required |
| brillouin-imaging-napari | Napari plugin for opening and exploring brim files within the napari image viewer |
| brillouin-imaging-fiji | ImageJ/Fiji plugin for opening brim files directly in ImageJ |
- View and analyze data in the browser: biobrillouin.org/brimview
- Read/write .brim files: prevedel-lab.github.io/brimfile
- Validate a brim file online (no installation needed): biobrillouin.org/brim-validator
We welcome contributions, feedback, and extensions from the wider microscopy and bioimaging community. The file format specification is open for discussion — please open an issue in Brillouin-standard-file to propose changes or raise questions. For bugs and feature requests in individual tools, open an issue in the relevant repository. For general discussion about the brim ecosystem, you can start a discussion in the Brillouin imaging organization.
We also encourage commercial Brillouin microscope manufacturers to adopt and contribute to this open standard.
