DOI: 10.5281/zenodo.15682921
title: Synchrotron radiation-based micro computed tomography dataset - in vivo mouse brain - Mouse63

description: Intra-cerebroventricular infusion at ESRF ID17 beamline

This datasets features a synchrotron radiation-based micro computed tomography dataset of a C57BL/6J mouse injected with barium-based contrast agent into the lateral ventricle. Data was recorded at the beamline ID17 of the European Synchrotron Radiation Facility in June 2022. For more information, see the associated publication, repository or the FABRIC4 portal.



mouse63_female_alive_22p8g_0p2ulmin_1ul_2KTimeResolved_thirdventricle_timeseries2_001.zipFull 3D-stack, time point 1, start of contrast agent infusion

mouse63_female_alive_22p8g_0p2ulmin_1ul_2KTimeResolved_thirdventricle_timeseries2_019.zipFull 3D-stack, time point 19, 9 min after start of contrast agent infusion

mouse63_female_alive_22p8g_0p2ulmin_1ul_2KTimeResolved_thirdventricle_timeseries2_slice300_timesteps001-100.zip2D slice z = 300, all time points

mouse63_female_alive_22p8g_0p2ulmin_1ul_2KTimeResolved_thirdventricle_timeseries2_slice300_timesteps001-100_registered.zip2D slice z = 300, all time points, registered and transformed tomograms

mouse63_female_alive_22p8g_0p2ulmin_1ul_2KTimeResolved_thirdventricle_timeseries2_slice600_timesteps001-100.zip2D slice z = 600, all time points

Supplementary_Video_2.mp42D slice z = 300, all time steps, registered and transformed tomographs

Supplementary_Video_3.mp42D radiographs, projection angle = 0°, all time points


Methods

For the dataset shown, a female mouse (SubjectID: Mouse63) twelve weeks of age and 22.8 g body weight was first injected subcutaneously with buprenorphine (0.1 mg/kg) for analgesia. Anesthesia was induced after onset of analgesia thirty 30  minutesmin later, via intraperitoneal injection of a cocktail of ketamine (73 mg/kg) &and medetomidine (0.18 mg/kg). The depth of anesthesia was monitored by testing reflexes, and additional injections of the same anesthetic mixture were given as needed. During imaging, this was done via an intraperitoneal infusion line (30 G needle with 0.28 mm inner diameter tubing) connected to a remote-controlled syringe pump. Eye ointment was applied and the skull, neck, and upper thoracic region of the mouse were shaved to avoid potential artifactartefacts during X-ray imaging. 2 × 0.5 ml glucose 10 % was administered in two separate subcutaneous injections, and tracheotomy was performed using a metal tracheal cannula with Y-adapter for artificial ventilation. Before the start of infusion implant surgery, syringes and tubing were mounted into the syringe pump and filled with mineral oil as a hydraulic fluid.

The mouse was then secured in a stereotactic frame and ventilated with a MiniVent, providing oxygen-enriched air. The exhaled air was routed through a water column to maintain 2 cmH2O positive end-expiratory pressure. Stroke volume was set to 125 µl, respiration rate to 150 bpm.

For cannula implantation, excess periosteum from the bone was removed and the bregma was identified. A small hole of about 1 mm diameter was drilled through the parietal bone at the injection coordinates. An MRI-compatible PEEK infusion cannula of 2.3 mm length was filled with 1.5× concentrated contrast agent (480 mg Ba/ml) and implanted into the right lateral ventricle. Cannula coordinates were 0.95 mm lateral and 0.22 mm caudal of the bregma.

The animal was then transferred to the radiation hutch containing the SRµCT imaging setup described above, where it was imaged with a monochromatic beam at a photon energy of 37.5 keV. 2000 radiographs over a rotation range of 360° were acquired with a pco.edge 5.5 detectorcamera coupled with a Hasselblad 100 mm f/2.2 lens and a 250 µm LuAG:Ce scintillator for 6.45 µm effective pixel size. The field of view was reduced to 2560 × 700 pixels due to the limited height of the X-ray beam, and recorded with 4 ms exposure time and 1 ms overhead time. Acquisition time per scan was 10 s. Sample-detector distance was 2.5 m. 

The animal was infused with contrast agent while one tomographic scan was acquired every 30 seconds for 50 min. 1 µl of contrast agent were infused at rate of 0.2 µl/min in the first 5 min of the acquisition, then infusion was stopped. Flat-field images were only acquired at the beginning and the end of the 100 scans.

Tomograms were reconstructed using the ESRF software Nabu (version 2023.2.0), which is based on and its filtered backprojection algorithm. Ring artefact removal was performed via stripe removal in the sinograms using a combined wavelet-Fourier filtering. The center of rotation for each reconstruction was manually fine-tuned. Image intensity values were scaled with a correction factor to account for an incorrect voxel size written into the metadata during image acquisition.

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 driven by maximizing normalized cross-correlation as an image similarity measure within the extended bone mask. Automatic image registration used the open-source software elastix (version 4.9). Images were rescaled to the intensity range in the 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.

Due to an incorrect voxel size of 6.0 µm being entered in the metadata and used during reconstruction, the intensity values in the datasets provided were multiplied by 6.0 µm / 6.45 µm = 0.930 after reconstructions so that the intensity values correspond to linear attenuation coefficients.