DOI: 10.5281/zenodo.15674075
title: Synchrotron radiation-based micro computed tomography dataset - in vivo mouse brain - Mouse19 - Paganin

description: Contrast agent-free imaging at ESRF ID17 beamline

This datasets features a synchrotron radiation-based micro computed tomography dataset of a C57BL/6J mouse. Data was recorded at the beamline ID17 of the European Synchrotron Radiation Facility in November 2021. For more information, see the associated publication, repository or the FABRIC4 portal.



Mouse19_male_live_26p9_noCA_2k_h1_paganin.zipFull 3D-stack, heightstep 1, Paganin phase retrieval

Mouse19_male_live_26p9_noCA_2k_h2_paganin.zipFull 3D-stack, heightstep 2, Paganin phase retrieval


Methods

C57BL/6J mice (strain code 632) were supplied by Charles River Laboratoire France. To ensure proper acclimatization, the animals were housed within the local animal facility for at least one week before the experiments. All procedures adhered to the European guidelines for animal experimentation (2010/63/UE). The experimental protocols were reviewed and approved by the responsible French ethics committee Comité d’éthique en expérimentation animale de l’ESRF (ETHAX), approval number: APAFIS 30913-2021040211343677 v1.

For the dataset shown, a male mouse (SubjectID: Mouse19) twelve weeks of age and 26.9 g body weight was first injected subcutaneously with buprenorphine (0.1 mg/kg of body weight) for analgesia. Anesthesia was induced after onset of analgesia 30 min later, via intraperitoneal injection of a cocktail of ketamine (73 mg/kg) and medetomidine (0.18 mg/kg). The animals were kept in a custom-made warmed box at 33 °C during anesthesia induction. The depth of anesthesia was monitored by testing reflexes, and additional injections were given as needed. During imaging, this was done via an intraperitoneal infusion line (30G 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 artefacts during X-ray imaging. 2 × 0.5 ml glucose 10% was administered in two separate subcutaneous injections, and tracheotomy surgery was performed, where a metal tracheal cannula with Y-adapter (outer diameter 1.0 mm, length 13 mm, depending on size of the animal. Hugo Sachs Elektronik, March-Hugstetten, Germany) was inserted into the trachea for artificial ventilation.

The animal was then transferred to the radiation hutch, where it was imaged with a monochromatic beam at a photon energy of 37.95 keV. 2 000 radiographs over a rotation range of 180° were acquired with a pco.edge 5.5 camera coupled to a Hasselblad 100 mm f/2.2 lens and a 250 µm LuAG:Ce scintillator for 6.3 µm effective pixel size. The field of view was reduced to 2560 × 780 pixels (16.1 mm × 4.9 mm) due to the limited height of the X-ray beam. Images were recorded with 5 ms exposure time and 5 ms overhead time. Acquisition time per scan was 20 s. The distance between sample and detector was 3 m.

Tomograms were reconstructed using GPU-accelerated filtered backprojection, implemented in the ASTRA Toolbox (version 2.1.0), and accessed through TomoPy (version 1.12.2). Propagation-based phase retrieval introduced by Paganin et al. was applied using a δ/β parameter of 200.