ArticleBMC medical imaging2018
High-definition neural visualization of rodent brain using micro-CT scanning and non-local-means processing.
Article in BMC medical imaging, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 26 citations in OpenAlex.
- Head of the Syrian Hamster (Animals : an open access journal from MDPI · 2026Article
- Detailed microCT imaging protocol for ex vivo rat stomachs with comparative analysis.Scientific reports · 2025Article
- Lateralization of Hippocampal Dentate Spikes and Sharp-Wave Ripples in Urethane Anesthetized Rats Depends on Cholinergic Tone.Hippocampus · 2025Article
- Comparing microCT Staining and Scanning Methodology for Brain Studies in Various Sizes of Spiders.The Journal of comparative neurology · 2025Article
- The SmARTR pipeline: A modular workflow for the cinematic rendering of 3D scientific imaging data.iScience · 2024Article
- Integrating multimodality magnetic resonance imaging to the Allen Mouse Brain Common Coordinate Framework.NMR in biomedicine · 2023Article
- Revealing the three-dimensional murine brain microstructure by contrast-enhanced computed tomography.Frontiers in neuroscience · 2023Article
- High-resolution micro-CT for 3D infarct characterization and segmentation in mice stroke models.Scientific reports · 2022Article
- Micro-CT yields high image quality in human fetal post-mortem imaging despite maceration.BMC medical imaging · 2021Article
- Advances in micro-CT imaging of small animals.Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics (AIFB) · 2021Review
- Brain size reductions associated with endothelin B receptor mutation, a cause of Hirschsprung's disease.BMC neuroscience · 2021Article
- Human fetal whole-body postmortem microfocus computed tomographic imaging.Nature protocols · 2021Article
- Iodine staining outperforms phosphotungstic acid in high-resolution micro-CT scanning of post-natal mice cardiac structures.Journal of medical imaging (Bellingham, Wash.) · 2021Article
- Micro-computed tomography with contrast enhancement: An excellent technique for soft tissue examination in humans.PloS one · 2021Article
- Acute administration of diazepam or midazolam minimally alters long-term neuropathological effects in the rat brain following acute intoxication with diisopropylfluorophosphate.European journal of pharmacology · 2020Article
- ViceCT and whiceCT for simultaneous high-resolution visualization of craniofacial, brain and ventricular anatomy from micro-computed tomography.Scientific reports · 2020Article
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMicro-CT holds promising potential for phenotyping and histological purposes. However, few have clarified the difference in the neuroimaging quality between ex vivo and in vivo micro-CT scanners. In addition, no direct comparison has been made between micro-CT scans and standard microscopy. Furthermore, while the efficacy of various stains for yielding soft-tissue contrast in CT scans have been compared in other studies for embryos, staining protocols for larger samples have yet to be clarified. Lastly, post-acquisition processing for image enhancements have not been addressed.
methodsComparisons of postnatal rat brain micro-CT scans obtained through custom-built ex vivo and commercially available in vivo micro-CT scanners were made. Subsequently, the scanned rat brains were then H&E stained for microscopy. Neuroanatomy on micro-CT scanning and 4× microscopy of rat brain were compared. Diffusion and perfusion staining using iodine or PTA were trialled on adult and neonatal encapsulated rat brains. Different combinations of stain concentration and staining time were trialled. Post-acquisition denoising with NLM filter was completed using a modern General-Purpose Graphic Processing Unit (GPGPU) and custom code for prompt processing.
resultsEx vivo micro-CT scans of iodine-stained postnatal rat brains yields 3D images with details comparable to 4× H&E light micrographs. Neural features shown on ex vivo micro-CT scans were significantly more distinctive than those on in vivo micro-CT scans. Both ex vivo and in vivo micro-CT scans required diffusion staining through small craniotomy. Perfusion staining is ineffective. Iodine staining was more efficient than PTA in terms of time. Consistently, enhancement made by NLM denoising on in vivo micro-CT images were more pronounced than that on ex vivo micro-CT scans due to their difference in image signal-to-noise indexes.
conclusionsMicro-CT scanning is a powerful and versatile visualization tool available for qualitative and potential quantitative anatomical analysis. Simple diffusion staining via craniotomy with 1.5% iodine is an effective and minimal structural-invasive method for both in vivo and ex vivo micro-CT scanning for studying the microscopic morphology of neonatal and adult rat brains. Post-acquisition NLM filtering is an effective enhancement technique for in vivo micro-CT brain scans.
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