Development and Implementation of a Corriedale Ovine Brain Atlas for Use in Atlas-Based Segmentation

Abstract

Segmentation is the process of partitioning an image into subdivisions and can be applied to medical images to isolate anatomical or pathological areas for further analysis. This process can be done manually or automated by the use of image processing computer packages. Atlas-based segmentation automates this process by the use of a pre-labelled template and a registration algorithm. We developed an ovine brain atlas that can be used as a model for neurological conditions such as Parkinson’s disease and focal epilepsy. 17 female Corriedale ovine brains were imaged in-vivo in a 1.5T (low-resolution) MRI scanner. 13 of the low-resolution images were combined using a template construction algorithm to form a low-resolution template. The template was labelled to form an atlas and tested by comparing manual with atlas-based segmentations against the remaining four low-resolution images. The comparisons were in the form of similarity metrics used in previous segmentation research. Dice Similarity Coefficients were utilised to determine the degree of overlap between eight independent, manual and atlas-based segmentations, with values ranging from 0 (no overlap) to 1 (complete overlap). For 7 of these 8 segmented areas, we achieved a Dice Similarity Coefficient of 0.5–0.8. The amygdala was difficult to segment due to its variable location and similar intensity to surrounding tissues resulting in Dice Coefficients of 0.0–0.2. We developed a low resolution ovine brain atlas with eight clinically relevant areas labelled. This brain atlas performed comparably to prior human atlases described in the literature and to intra-observer error providing an atlas that can be used to guide further research using ovine brains as a model and is hosted online for public access.

Establishing sheep as an experimental species to validate ultrasound-mediated blood-brain barrier opening for potential therapeutic interventions

“…Brain size is broadly similar between these species and, unlike rodents, all have a gyrencephalic brain ( Figure 1 ). Sheep represent an attractive model because their skull thickness and composition are similar to those of humans, they are readily available, relatively easy to use experimentally, and brain atlases are well documented for this species 49 . Sheep also have a body weight profile closer to humans and this is useful for optimizing microbubble kinetics and dosing in relation to BBB opening.…”

CRISPR/Cas9 mediated generation of an ovine model for infantile neuronal ceroid lipofuscinosis (CLN1 disease)

“…In the absence of a bespoke template and atlas for the specific breed used here the University of Melbourne Corriedale ovine atlas from Liyanage et al . was chosen, since this contained regions of interest (ROI) relevant to the expected areas of pathological brain involvement 40 . The Melbourne template does not include a T2w image, however, and a template including a brain-extracted T2w from INRA (Institut National de Recherche Agronomique, France) was chosen to improve accuracy of template-based segmentation 41 .…”

“…The Melbourne template does not include a T2w image, however, and a template including a brain-extracted T2w from INRA (Institut National de Recherche Agronomique, France) was chosen to improve accuracy of template-based segmentation 41 . The Melbourne template was warped into INRA T1w template space using ANTs (Advanced Normalization Tools, Penn Image Computing & Science Lab, University of Pennsylvania, USA) diffeomorphic registration with affine and SyN algorithms, and cross correlation similarity metric 40–43 . The resultant series of transforms produced the Melbourne atlas regions of interest in INRA template space.…”

In vivo Diffusion Tensor Magnetic Resonance Tractography of the Sheep Brain: An Atlas of the Ovine White Matter Fiber Bundles

“…Finally, the possible inaccuracy derived from anatomical variability of the animals may be improved even considering other ovine breeds. Future investigation will be aimed at exploring the degree of heterogeneity in brain anatomy between different ovine varieties, possibly leading toward a more accurate representation of pivotal neuroanatomical structures in exceptionally detailed atlases (53).…”