Microtomography of a mouse brain from formalin fixed to paraffin embedded: datasets and registration parameters

Hard X-ray microtromography datasets of a single mouse brain immersed in formalin, 50%, 70%, 80%, 90%, 100% ethanol, and xylene, as well as embedded in a paraffin block. Three-dimensional datasets have a voxel length of 9.3 microns. These datasets were the basis for two papers published in Journal of Neuroscience Methods (doi: 10.1016/j.jneumeth.2021.109354 and 10.1016/j.jneumeth.2021.109385), where the volumetric strain fields and density changes were determined within a mouse brain during embedding. Transform parameter files are given in order to apply a registration to a common coordinate system. Registration settings are also given, so that registration can be modified. Transformations and registrations are both based on the open source software elastix (and transformix). The formalin dataset should be transformed with t0.txt, the others with t3_NAME.txt (e.g. transformix -in ./100pethanol_bin3.mha -tp ./t3_100pethanol.txt -out OUTPUT_LOCATION). The volumes should be unzipped first. To recover X-ray absorption coefficient (µ, linear attenuation coefficient), map the 16-bit integer values [-32768,32767] of the datasets to absorption coefficient values [-0.4746,2.373] cm^-1. Imaging was performed at the ANATOMIX Beamline of Synchrotron SOLEIL (Gif-sur-Yvette, France). This represents the \(3\times3\times3\) binned datasets, as full resolution datasets are too large for easy handling. Please contact the authors to request access to portions of the full resolution data. If any part of these datasets are used, please cite the two related papers: 10.1016/j.jneumeth.2021.109354 and 10.1016/j.jneumeth.2021.109385.