Priority U-Net: Detection of Punctuate White Matter Lesions in Preterm Neonate in 3D Cranial Ultrasonography

Pierre Erbacher, Carole Lartizien, Matthieu Martin, Pedro Foletto-Pimenta, Philippe Quetin, Philippe Delachartre
; Proceedings of the Third Conference on Medical Imaging with Deep Learning, PMLR 121:205-216, 2020.

Abstract

About $18-35%$ of the preterm infants suffer from punctuate white matter lesion (PWML). Accurately assessing the volume and localisation of these lesions at the early postnatal phase can help paediatricians adapting the therapeutic strategy and potentially reduce severe sequelae. MRI is the gold standard neuroimaging tool to assess minimal to severe WM lesions, but it is only rarely performed for cost and accessibility reasons. Cranial ultrasonography (cUS) is a routinely used tool, however, the visual detection of PWM lesions is challenging and time consuming due to speckle noise and low contrast image. In this paper we perform semantic detection and segmentation of PWML on 3D cranial ultrasonography. We introduce a novel deep architecture, called Priority U-Net, based on the 2D U-Net backbone combined with the self balancing focal loss and a soft attention model focusing on the PWML localisation. The proposed attention mask is a 3D probabilistic map derived from spatial prior knowledge of PWML localisation computed from our dataset. We compare the performance of the priority U-Net with the U-Net baseline based on a dataset including 21 exams of preterm neonates (131 PWMLs). We also evaluate the impact of the self-balancing focal loss (SBFL) on the performance. Compared to the U-Net, the priority U-Net with SBFL increases the recall and the precision in the detection task from 0.4404 to 0.5370 and from 0.3217 to 0.5043, respectively. The Dice metric is also increased from 0.3040 to 0.3839 in the segmentation task.

Cite this Paper


BibTeX
@InProceedings{pmlr-v121-erbacher20a, title = {Priority U-Net: Detection of Punctuate White Matter Lesions in Preterm Neonate in 3D Cranial Ultrasonography}, author = {Erbacher, Pierre and Lartizien, Carole and Martin, Matthieu and Foletto-Pimenta, Pedro and Quetin, Philippe and Delachartre, Philippe}, pages = {205--216}, year = {2020}, editor = {Tal Arbel and Ismail Ben Ayed and Marleen de Bruijne and Maxime Descoteaux and Herve Lombaert and Christopher Pal}, volume = {121}, series = {Proceedings of Machine Learning Research}, address = {Montreal, QC, Canada}, month = {06--08 Jul}, publisher = {PMLR}, pdf = {http://proceedings.mlr.press/v121/erbacher20a/erbacher20a.pdf}, url = {http://proceedings.mlr.press/v121/erbacher20a.html}, abstract = {About $18-35%$ of the preterm infants suffer from punctuate white matter lesion (PWML). Accurately assessing the volume and localisation of these lesions at the early postnatal phase can help paediatricians adapting the therapeutic strategy and potentially reduce severe sequelae. MRI is the gold standard neuroimaging tool to assess minimal to severe WM lesions, but it is only rarely performed for cost and accessibility reasons. Cranial ultrasonography (cUS) is a routinely used tool, however, the visual detection of PWM lesions is challenging and time consuming due to speckle noise and low contrast image. In this paper we perform semantic detection and segmentation of PWML on 3D cranial ultrasonography. We introduce a novel deep architecture, called Priority U-Net, based on the 2D U-Net backbone combined with the self balancing focal loss and a soft attention model focusing on the PWML localisation. The proposed attention mask is a 3D probabilistic map derived from spatial prior knowledge of PWML localisation computed from our dataset. We compare the performance of the priority U-Net with the U-Net baseline based on a dataset including 21 exams of preterm neonates (131 PWMLs). We also evaluate the impact of the self-balancing focal loss (SBFL) on the performance. Compared to the U-Net, the priority U-Net with SBFL increases the recall and the precision in the detection task from 0.4404 to 0.5370 and from 0.3217 to 0.5043, respectively. The Dice metric is also increased from 0.3040 to 0.3839 in the segmentation task.} }
Endnote
%0 Conference Paper %T Priority U-Net: Detection of Punctuate White Matter Lesions in Preterm Neonate in 3D Cranial Ultrasonography %A Pierre Erbacher %A Carole Lartizien %A Matthieu Martin %A Pedro Foletto-Pimenta %A Philippe Quetin %A Philippe Delachartre %B Proceedings of the Third Conference on Medical Imaging with Deep Learning %C Proceedings of Machine Learning Research %D 2020 %E Tal Arbel %E Ismail Ben Ayed %E Marleen de Bruijne %E Maxime Descoteaux %E Herve Lombaert %E Christopher Pal %F pmlr-v121-erbacher20a %I PMLR %J Proceedings of Machine Learning Research %P 205--216 %U http://proceedings.mlr.press %V 121 %W PMLR %X About $18-35%$ of the preterm infants suffer from punctuate white matter lesion (PWML). Accurately assessing the volume and localisation of these lesions at the early postnatal phase can help paediatricians adapting the therapeutic strategy and potentially reduce severe sequelae. MRI is the gold standard neuroimaging tool to assess minimal to severe WM lesions, but it is only rarely performed for cost and accessibility reasons. Cranial ultrasonography (cUS) is a routinely used tool, however, the visual detection of PWM lesions is challenging and time consuming due to speckle noise and low contrast image. In this paper we perform semantic detection and segmentation of PWML on 3D cranial ultrasonography. We introduce a novel deep architecture, called Priority U-Net, based on the 2D U-Net backbone combined with the self balancing focal loss and a soft attention model focusing on the PWML localisation. The proposed attention mask is a 3D probabilistic map derived from spatial prior knowledge of PWML localisation computed from our dataset. We compare the performance of the priority U-Net with the U-Net baseline based on a dataset including 21 exams of preterm neonates (131 PWMLs). We also evaluate the impact of the self-balancing focal loss (SBFL) on the performance. Compared to the U-Net, the priority U-Net with SBFL increases the recall and the precision in the detection task from 0.4404 to 0.5370 and from 0.3217 to 0.5043, respectively. The Dice metric is also increased from 0.3040 to 0.3839 in the segmentation task.
APA
Erbacher, P., Lartizien, C., Martin, M., Foletto-Pimenta, P., Quetin, P. & Delachartre, P.. (2020). Priority U-Net: Detection of Punctuate White Matter Lesions in Preterm Neonate in 3D Cranial Ultrasonography. Proceedings of the Third Conference on Medical Imaging with Deep Learning, in PMLR 121:205-216

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