Gel Phantom: Dynamic X-Ray Tomography for Plant Stem Diffusion Simulation

Gel phantom data simulates the diffusion of iodine-based contrast agents inside plant stems using X-ray microtomography. The dataset contains 17 primary time frames of 2D fan-beam projections, with reconstructions available at 256x256 and 512x512 pixel resolutions. It is structured for testing tomographic reconstruction algorithms and includes example codes requiring MATLAB toolboxes like ASTRA and HelTomo.

Use Cases

• Benchmarking tomographic reconstruction algorithms based on time-series projection data.
• Simulating and studying diffusion processes in plant vascular systems using the gel phantom model.
• Testing forward operators and reconstruction pipelines with included MATLAB toolboxes and metadata.

Strengths

• Provides 17 consecutive time frames capturing diffusion dynamics, plus an additional 18th frame for extended analysis.
• Includes data at two reconstruction resolutions (256x256 and 512x512) for flexibility in algorithm testing.
• Contains detailed metadata structures and example codes for immediate application with standard MATLAB toolboxes.

Limitations

• Specific row counts, file sizes, and last update dates are not provided across any source.
• Relies on specific MATLAB toolbox versions (e.g., HelTomo v1), with noted metadata incompatibility with newer versions.
• Dataset scope is limited to a single, controlled phantom experiment rather than diverse biological samples.

Provenance

Source

University of Helsinki, created by Tommi Heikkilä.

Collection Method

Constructed using a 50 ml Falcon test tube filled with agarose gel, with cavities filled with sucrose solution and punctured plastic straws to simulate plant cellular structures. Data captured via a fanbeam microCT-scanner.