DOI: 10.5281/zenodo.15671361
title: Synchrotron radiation-based micro computed tomography dataset - in vivo mouse brain - JP34

description: Contrast agent-free imaging of peri-mortem morphological changes at SPring-8 BL20B2 beamline

This datasets features a synchrotron radiation-based micro computed tomography dataset of a C57BL/6JJmsSLC mouse. Data was recorded at the beamline BL20B2 of the synchrotron SPring-8 in May 2023. For more information, see the associated publication, repository or the FABRIC4 portal.



JP34-invivo-scan4-60scans-brain_001.zipFull 3D-stack, time point 1

JP34-invivo-scan4-60scans-brain_ROI_Slice0380_registered.zip2D slice z = 380, all time points, registered and transformed tomographs

Supplementary_Video_1.mp42D slice z = 380, all time points, registered and transformed tomographs


Methods

C57BL/6JJmsSLC mice (Japan SLC, Inc.) were used for all experiments at the BL20B2 beamline. To ensure proper acclimatization, animals were housed in the local animal facility and habituated to non-aversive handling techniques for 10 days prior to the experiments. The experimental protocols were reviewed and approved by the responsible ethics committee of SPring-8.

For the dataset shown, a female mouse (SubjectID: JP34) twelve weeks of age and 19.2 g body weight was first anesthesized with a cocktail of medetomidine (0.3 mg/kg), midazolam (4 mg/kg) and butorphanol (5 mg/kg). Eye ointment was applied and the skull, neck, and upper thoracic region of the mouse were shaved to avoid phase artefacts during X-ray imaging. The animal was then transferred to the imaging hutch without further surgeries, and injected with a five-fold overdose of the above anesthetic cocktail for euthanasia immediately before starting the imaging procedure (3 min).

A total of 1800 radiographs were acquired over a 180° rotation using a Hamamatsu Orca Flash4.0 v2 camera coupled to a tandem lens system (105 mm f/2.4 and 85 mm f/1.4) and a 500 µm LuAG:Ce scintillator, yielding an effective pixel size of 7.92 µm. The detector field of view was limited by the vertical extent of the beam, resulting in an effective field of view of 2048 × 1500 pixels (16.4 mm × 12.0 mm). Images were acquired with an exposure time of 4 ms and an inter-projection overhead of 9 ms, resulting in a total scan time of 23 s. The rotation stage returned to the start position in 9 s and the next scan was started after a delay of 8 s, meaning one time step was acquired every 40 s. 60 time steps were recorded over 40 min. The sample-to-detector distance was 3 m. Tomograms were reconstructed using the BL20B2 in-house reconstruction software, ct-rec (version 2023.05.03), with automatic center-of-rotation determination. Output image intensity values directly correspond to linear attenuation coefficients.

In order to isolate potential motion of the ventricles from the effect of whole animal motion, data volumes of the different time points used for comparison were registered to the first reconstruction of the series (called reference image) via rigid registration. An extended bone mask without ventricular spaces was created for the reference image to ensure that the contrast enhancement of the ventricles would not affect registration. The registration was mostly driven by maximizing normalized cross-correlation as an image similarity measure within the extended bone mask. Note the registrations for time steps 28, 29 and 60 were registered using mutual information MI as the registration with correlation coefficient was not satisfactory, i.e. final value below 0.7. Automatic image registration used the open-source software elastix (version 4.9). Images were rescaled to the intensity range in the region-of-interest (ROI) of the reference image to reduce quantification errors when using 256 bins for covering the intensity range during registration. Images of the original intensities were afterwards transformed based on the registration result.