Saved in:
| Main Authors: | , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Preprint |
| Published: |
2024
|
| Subjects: | |
| Online Access: | https://arxiv.org/abs/2405.08337 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1866916249926107136 |
|---|---|
| author | Sinclair, Benjamin Vivash, Lucy Moses, Jasmine Lynch, Miranda Pham, William Dorfman, Karina Marotta, Cassandra Koh, Shaun Bunyamin, Jacob Rowsthorn, Ella Jarema, Alex Peiris, Himashi Chen, Zhaolin Shultz, Sandy R Wright, David K Kong, Dexiao Naismith, Sharon L. OBrien, Terence J. Law, Meng |
| author_facet | Sinclair, Benjamin Vivash, Lucy Moses, Jasmine Lynch, Miranda Pham, William Dorfman, Karina Marotta, Cassandra Koh, Shaun Bunyamin, Jacob Rowsthorn, Ella Jarema, Alex Peiris, Himashi Chen, Zhaolin Shultz, Sandy R Wright, David K Kong, Dexiao Naismith, Sharon L. OBrien, Terence J. Law, Meng |
| contents | Perivascular spaces(PVSs) form a central component of the brainś waste clearance system, the glymphatic system. These structures are visible on MRI images, and their morphology is associated with aging and neurological disease. Manual quantification of PVS is time consuming and subjective. Numerous deep learning methods for PVS segmentation have been developed, however the majority have been developed and evaluated on homogenous datasets and high resolution scans, perhaps limiting their applicability for the wide range of image qualities acquired in clinic and research. In this work we train a nnUNet, a top-performing biomedical image segmentation algorithm, on a heterogenous training sample of manually segmented MRI images of a range of different qualities and resolutions from 6 different datasets. These are compared to publicly available deep learning methods for 3D segmentation of PVS. The resulting model, PINGU (Perivascular space Identification Nnunet for Generalised Usage), achieved voxel and cluster level dice scores of 0.50(SD=0.15), 0.63(0.17) in the white matter(WM), and 0.54(0.11), 0.66(0.17) in the basal ganglia(BG). Performance on data from unseen sites was substantially lower for both PINGU(0.20-0.38(WM, voxel), 0.29-0.58(WM, cluster), 0.22-0.36(BG, voxel), 0.46-0.60(BG, cluster)) and the publicly available algorithms(0.18-0.30(WM, voxel), 0.29-0.38(WM cluster), 0.10-0.20(BG, voxel), 0.15-0.37(BG, cluster)), but PINGU strongly outperformed the publicly available algorithms, particularly in the BG. Finally, training PINGU on manual segmentations from a single site with homogenous scan properties gave marginally lower performances on internal cross-validation, but in some cases gave higher performance on external validation. PINGU stands out as broad-use PVS segmentation tool, with particular strength in the BG, an area of PVS related to vascular disease and pathology. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2405_08337 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Perivascular space Identification Nnunet for Generalised Usage (PINGU) Sinclair, Benjamin Vivash, Lucy Moses, Jasmine Lynch, Miranda Pham, William Dorfman, Karina Marotta, Cassandra Koh, Shaun Bunyamin, Jacob Rowsthorn, Ella Jarema, Alex Peiris, Himashi Chen, Zhaolin Shultz, Sandy R Wright, David K Kong, Dexiao Naismith, Sharon L. OBrien, Terence J. Law, Meng Computer Vision and Pattern Recognition Artificial Intelligence Perivascular spaces(PVSs) form a central component of the brainś waste clearance system, the glymphatic system. These structures are visible on MRI images, and their morphology is associated with aging and neurological disease. Manual quantification of PVS is time consuming and subjective. Numerous deep learning methods for PVS segmentation have been developed, however the majority have been developed and evaluated on homogenous datasets and high resolution scans, perhaps limiting their applicability for the wide range of image qualities acquired in clinic and research. In this work we train a nnUNet, a top-performing biomedical image segmentation algorithm, on a heterogenous training sample of manually segmented MRI images of a range of different qualities and resolutions from 6 different datasets. These are compared to publicly available deep learning methods for 3D segmentation of PVS. The resulting model, PINGU (Perivascular space Identification Nnunet for Generalised Usage), achieved voxel and cluster level dice scores of 0.50(SD=0.15), 0.63(0.17) in the white matter(WM), and 0.54(0.11), 0.66(0.17) in the basal ganglia(BG). Performance on data from unseen sites was substantially lower for both PINGU(0.20-0.38(WM, voxel), 0.29-0.58(WM, cluster), 0.22-0.36(BG, voxel), 0.46-0.60(BG, cluster)) and the publicly available algorithms(0.18-0.30(WM, voxel), 0.29-0.38(WM cluster), 0.10-0.20(BG, voxel), 0.15-0.37(BG, cluster)), but PINGU strongly outperformed the publicly available algorithms, particularly in the BG. Finally, training PINGU on manual segmentations from a single site with homogenous scan properties gave marginally lower performances on internal cross-validation, but in some cases gave higher performance on external validation. PINGU stands out as broad-use PVS segmentation tool, with particular strength in the BG, an area of PVS related to vascular disease and pathology. |
| title | Perivascular space Identification Nnunet for Generalised Usage (PINGU) |
| topic | Computer Vision and Pattern Recognition Artificial Intelligence |
| url | https://arxiv.org/abs/2405.08337 |