Brillouin microscopy is rapidly emerging as a powerful technique for imaging the mechanical properties of biological specimens in a label-free, non-contact manner. Different approaches can be used to acquire the Brillouin signal (e.g. spontaneous, stimulated, time-domain) but ultimately they all collect a spectrum for each voxel in the image. For more information you can find many reviews about the topic, e.g. Kabakova et al 2024 and Prevedel et al. 2019
For images (and volumes and timelapses), we propose a Zarr-based standarized file format to store and analyse Brillouin microscopy data and metadata: .brim (Brillouin Image)
BrimView is an open-source tool that can read, display, explore and (re)analyze these brim files.
Test the online version by clicking here. 4 different dataset, from different Brillouin acquisition methods, are available on public S3-buckets.
Use the sidebar to load some data, and then explore the different timepoints of the acquired volumes. Clicking on a pixel displays the underlaying acquired spectra.
If you want to get more information about this project, you can read our recent prepint.
Thanks to the data exploration and web app framework Panel, the same python code can be used to generate different app versions:
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Web version: runs entirely in the browser using Pyodide and WebAssembly (WASM). It is ideal for quickly inspecting .brim datasets—e.g., assessing data quality—on any computer without requiring installation.
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Standalone application: A fully self-contained desktop version built using PyInstaller and PyWebview, suitable for offline use on lab workstations without requiring a Python environment. Pre-built binaries and source code are available in the releases
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Local Panel Server: This version runs as a local Python server, offering the highest performance and full access to the underlying code for advanced users. It supports custom workflows, batch processing, and direct modification of the visualization or analysis pipeline.
| Local installation required | Internet access required | Performance | Customizability | |
|---|---|---|---|---|
| Web application | ❌ | ✔️ (to load the page) |
⭐ (impossible to edit files) |
⭐ |
| Standalone application | ❌ | ❌ | ⭐⭐ | ⭐ |
| Local Panel server | ✔️ | ❌ | ⭐⭐⭐ | ⭐⭐⭐ |
Read through this guide to install the necessary dependencies, and start working on customizing BrimView.
Contributions, issue reports, and feature requests are welcome via this GitHub repository.
Sebastian Hambura and Carlo Bevilacqua at Prevedel lab.
BrimView is completely free and open-source. It is licensed under the LGPL-3.0 license.