Synchrotron-based visualization and segmentation of elastic lamellae in the mouse carotid artery during quasi-static pressure inflation

This dataset contains images that were obtained during quasi-static pressure inflation of mouse carotid arteries. Images were taken with phase propagation imaging at the X02DA TOMCAT beamline of the Swiss Light Source synchrotron at the Paul Scherrer Institute in Villigen, Switzerland. Scans of n=12 left carotid arteries (n-6 Apoe-deficient mice, n=6 wild-type mice, all on a C57Bl6J background) were taken at pressure levels of 0, 10, 20, 30, 40, 50, 70, 90 and 120 mmHg. For analysis we selected 75 images from the center of each stack (starting at the center of the stack, and skipping 2 of every three images in both cranial and caudal axial directions) for each sample and for each pressure level, resulting in a total of 75 x 12 x 9 = 8100 analyzed images from 108 different scans. Segmentation, 3D visualization and geometric analysis is presented in the corresponding manuscript. Files are uploaded in 16bit .tif format and are named: mouseid_pressurelevel_stacknumber, with mouseid consisting of either Apoe (Apoe-deficient) or Bl (wild-type) and the mouse number, pressurelevel varies from P0 to P120 and stacknumber indicates which image from the stack has been uploaded

Propagation-based phase-contrast synchrotron imaging of aortic dissection in mice : from individual elastic lamella to 3D analysis

In order to show the advantage and potential of propagation-based phase-contrast synchrotron imaging in vascular pathology research, we analyzed aortic medial ruptures in BAPN/AngII-infused mice, a mouse model for aortic dissection. Ascending and thoraco-abdominal samples from n = 3 control animals and n = 10 BAPN/AngII-infused mice (after 3, 7 and 14 days of infusion, total of 24 samples) were scanned. A steep increase in the number of ruptures was already noted after 3 days of BAPN/AngII-infusion. The largest ruptures were found at the latest time points. 133 ruptures affected only the first lamella while 135 ruptures affected multiple layers. Medial ruptures through all lamellar layers, leading to false channel formation and intramural hematoma, occurred only in the thoraco-abdominal aorta and interlamellar hematoma formation in the ascending aorta could be directly related to ruptures of the innermost lamellae. The advantages of this technique are (i) ultra-high resolution that allows to visualize the individual elastic lamellae in the aorta; (ii) quantitative and qualitative analysis of medial ruptures; (iii) 3D analysis of the complete aorta; (iv) high contrast for qualitative information extraction, reducing the need for histology coupes; (v) earlier detection of (micro-) ruptures

A comparative evaluation of 3 different free-form deformable image registration and contour propagation methods for head and neck MRI : the case of parotid changes radiotherapy

Purpose: To validate and compare the deformable image registration and parotid contour propagation process for head and neck magnetic resonance imaging in patients treated with radiotherapy using 3 different approachesthe commercial MIM, the open-source Elastix software, and an optimized version of it. Materials and Methods: Twelve patients with head and neck cancer previously treated with radiotherapy were considered. Deformable image registration and parotid contour propagation were evaluated by considering the magnetic resonance images acquired before and after the end of the treatment. Deformable image registration, based on free-form deformation method, and contour propagation available on MIM were compared to Elastix. Two different contour propagation approaches were implemented for Elastix software, a conventional one (DIR_Trx) and an optimized homemade version, based on mesh deformation (DIR_Mesh). The accuracy of these 3 approaches was estimated by comparing propagated to manual contours in terms of average symmetric distance, maximum symmetric distance, Dice similarity coefficient, sensitivity, and inclusiveness. Results: A good agreement was generally found between the manual contours and the propagated ones, without differences among the 3 methods; in few critical cases with complex deformations, DIR_Mesh proved to be more accurate, having the lowest values of average symmetric distance and maximum symmetric distance and the highest value of Dice similarity coefficient, although nonsignificant. The average propagation errors with respect to the reference contours are lower than the voxel diagonal (2 mm), and Dice similarity coefficient is around 0.8 for all 3 methods. Conclusion: The 3 free-form deformation approaches were not significantly different in terms of deformable image registration accuracy and can be safely adopted for the registration and parotid contour propagation during radiotherapy on magnetic resonance imaging. More optimized approaches (as DIR_Mesh) could be preferable for critical deformations

Synchrotron-based phase contrast imaging of cardiovascular tissue in mice-grating interferometry or phase propagation?

Synchrotron-based x-ray phase-contrast imaging allows for detailed 3D insight into the microstructure of soft tissue and is increasingly used to improve our understanding of mouse models of cardiovascular disease. Two techniques dominate the field: grating interferometry, with superior density contrast at mid to lower microscopic resolutions, and propagation-based phase contrast, facilitating high-resolution tissue imaging. The choice between these techniques depends on which features one is interested in visualizing and is thus highly sample-dependent. In this manuscript we systematically evaluate the advantages and disadvantages of grating interferometry and propagation-based phase contrast for the specific application of pre-clinical cardiovascular tissue. We scanned samples obtained from 5 different mouse models of cardiovascular disease, ranging from carotid plaques over ascending and abdominal aortic aneurysms to hypertrophic hearts. Based on our findings we discuss in detail how synchrotron-based imaging can be used to increase our understanding of the anatomy and biomechanics of cardiovascular disease in mice. We also present a flowchart that can help future users to select the best synchrotron-based phase contrast technique for their pre-clinical cardiovascular samples

Analysis of serial CT images for studying the RT effects in head-neck cancer patients

Images taken during and after RT for head and neck cancer have the potential to quantitatively assess xerostomia. Image information may be used as biomarkers of RT effects on parotid glands with significant potential to support adaptive treatment strategies. We investigated the possibility to extract information based on in-room CT images (kVCT, MVCT), acquired for daily image-guided radiotherapy treatment of head-and-neck cancer patients, in order to predict individual response in terms of toxicity. Follow-up MRI images were also used in order to investigate long term parotid gland deformation