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Overview

VIBE

The VIBE platform provides high-performance computing resources designed to accelerate and streamline your bioimage analysis workflows.

Through a user-friendly graphical desktop interface (GUI) accessible directly from your browser, VIBE makes advanced computational resources available to all researchers at the University of Bern—no installation or specialized hardware required.

VIBE offers an integrated environment for working with microscopy datasets of any size. Whether you want to visualize multidimensional image stacks, explore large datasets, apply classical segmentation, or run custom deep-learning models for denoising or semantic segmentation, the platform provides the tools and performance you need.

The remote desktop includes a curated collection of widely used open-source applications from the bioimage analysis community, including Fiji, Napari, QuPath, Ilastik, Imod, Cellpose, and many others. All tools are preconfigured to work seamlessly with the platform’s storage and compute infrastructure, allowing you to focus on analysis rather than setup.

Who is it for?

The VIBE platform is designed for:

  • Biologists who need an easy and interactive yet powerful environment for visualization, segmentation and quantitative analysis.

  • Imaging specialists who support users and develop advanced pipelines.

  • Students and trainees who require a unified and standardized workspace for learning bioimage analysis.

  • Computational scientists running Python/R workflows or deep-learning models.

Key features

  • Fully Managed Remote Desktop: Access the entire environment via your web browser. No installation required. Works on Windows, Mac, and Linux.

  • Preinstalled Bioimage Analysis Tools: Fiji / ImageJ (with major plugins), Napari with visualization, segmentation and analysis plugins, QuPath for histology and whole-slide imaging, CellProfiler for batch image processing, Ilastik for interactive segmentation, Python (JupyterLab).

  • High-Performance Computing: Multi-core CPU nodes. Optional GPU-accelerated sessions for deep learning based segmentation. Large memory sessions for multi-GB image stacks.

  • Centralized Storage: Personal home folders. Project-based shared folders. Fast temporary scratch space. Direct integration with institutional storage systems (Research Storage).

  • Ready-to-Use and customizable workflows: Cell segmentation pipelines. 3D volumetric analysis workflows. Whole-slide imaging pipelines. Machine learning workflows using TensorFLow, Pytorch, etc.

User Requirements

To ensure smooth access to VIBE, users should meet the following technical and administrative requirements:

Technical Requirements

  • Any modern web browser.
  • Be connected to the UniBE campus network with a stable internet connection.
  • Device:
    • Laptop or desktop (Windows, macOS, or Linux)
    • Tablet is partially supported (mouse recommended)

Administrative Requirements

  • You must have:
    • Campus account.
    • UBELIX account.