Mouse Brain Microtomography Datasets from Formalin to Paraffin Embedding

Hard X-ray microtomography datasets of a single mouse brain at different stages of tissue processing, from formalin fixation to paraffin embedding. The three-dimensional datasets have a voxel length of 9.3 microns and were imaged at the ANATOMIX Beamline of Synchrotron SOLEIL in France. These datasets, provided by Griffin Rodgers of the University of Basel, were the basis for two papers published in the Journal of Neuroscience Methods in 2021.

Use Cases

• Analyzing volumetric strain fields within a mouse brain during embedding based on the provided 3D datasets.
• Studying density changes in brain tissue across different chemical immersions like ethanol and xylene.
• Applying and modifying image registration to a common coordinate system using the provided transform parameter files and elastix software settings.
• Recovering X-ray absorption coefficients by mapping the 16-bit integer values in the datasets.

Strengths

• Datasets have a defined voxel length of 9.3 microns, providing a specific spatial resolution.
• Includes transform parameter files and registration settings for aligning all datasets to a common coordinate system.
• Provides a specific mapping from 16-bit integer values to X-ray absorption coefficient values [-0.4746,2.373] cm⁻¹.

Limitations

• Description metadata is limited; actual data quality requires manual inspection after download.
• Column-level documentation is absent; field semantics must be inferred after download.
• The provided datasets are 3x3x3 binned versions; full-resolution data requires contacting the authors and may be too large for easy handling.

Provenance

Source

Imaging performed at the ANATOMIX Beamline of Synchrotron SOLEIL (Gif-sur-Yvette, France).

Collection Method

Hard X-ray microtomography of a single mouse brain through sequential chemical processing stages.

Geography

France