Volume rendering with BigDataViewer tools

Introduction

Key Features of BDV:

• Multi-resolution rendering: BDV supports multi-resolution pyramids, allowing fast, real-time exploration of large datasets.
• Arbitrary slicing: Enables users to zoom, rotate, and slice through datasets interactively and in any angle.
• Multiple data sources with individual transformations: Enables visualization of datasets consisting of multiple acquisitions.
• Comes preinstalled with Fiji.

BDV compatible formats

Supported Data Formats:

• HDF5/N5: These formats allow for hierarchical storage of large datasets, enabling faster access to the data and efficient memory usage.
• Any dataset Fiji compatible dataset: While these images might not support multi resolution rendering, they can still be imported into BDV to leverage arbitrary slicing.

Data conversion

BDV Plugin in Fiji

Conversion Steps:

• Step 1: Open your 3D image stack (e.g., TIFF) in Fiji.
• Step 2: Go to Plugins > BigDataViewer > Export Current Image as BDV.
• Step 3: Choose the output format (HDF5 or N5) and select any additional options (e.g., multi-resolution pyramid).

Data conversion

BigStitcher Plugin

Conversion Steps:

• Step 1: Follow the installation instructions.
• Step 2: Open Plugins › BigStitcher › BigStitcher
• Step 3: Click the Define a new dataset button on the left side of the dialog
• Step 4: Follow steps depending on your dataset type (more documentation linked below)

BigVolumeViewer (BVV)

Key Features

• GPU-accelerated rendering: BVV uses GPU processing to speed up the rendering of extremely large volumetric datasets.
• Multi-scale volume rendering: Allows for efficient exploration of datasets by loading data at different scales.
• available through Fiji BigVolumeViewer update site

BigVolumeViewer (BVV)

BigVolumeViewer - playground

• fork of BVV with additional features such as better volumetric rendering, gamma correction, lookup tables and more

SciView

Key Features of SciView:

• Interactive 3D rendering: Explore volumetric data interactively using SciView’s intuitive interface.
• Supports advanced lighting and shading: Create realistic 3D scenes with SciView’s lighting and shading options.

MultiModal Big Image Data Sharing and Exploration (MoBIE)

Key Features of MoBIE:

• Special focus on multimodal image datasets
• Can stream remote data
• Support of interactive tabular data exploration alongside images
• Integrated registration features

Paintera

Key Features of Paintera:

• Views of orthogonal 2D cross-sections
• Painting in 3D
• Mesh visualization and on-the-fly generation