Élodie Puybareau

High throughput automated detection of axial malformations in Medaka embryo

Abstract

Fish embryo models are widely used as screening tools to assess the efficacy and/or toxicity of chemicals. This assessment involves the analysis of embryo morphological abnormalities. In this article, we propose a multi-scale pipeline to allow automated classification of fish embryos (Medaka: Oryzias latipes) based on the presence or absence of spine malformations. The proposed pipeline relies on the acquisition of fish embryo 2D images, on feature extraction based on mathematical morphology operators and on machine learning classification. After image acquisition, segmentation tools are used to detect the embryo before analysing several morphological features. An approach based on machine learning is then applied to these features to automatically classify embryos according to the presence of axial malformations. We built and validated our learning model on 1459 images with a 10-fold cross-validation by comparison with the gold standard of 3D observations performed under a microscope by a trained operator. Our pipeline results in correct classification in 85% of the cases included in the database. This percentage is similar to the percentage of success of a trained human operator working on 2D images. The key benefit of our approach is the low computational cost of our image analysis pipeline, which guarantees optimal throughput analysis..

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High throughput automated detection of axial malformations in fish embryo

Abstract

Fish embryo models are widely used as screening tools to assess the efficacy and /or toxicity of chemicals. This assessment involves analysing embryo morphological abnormalities. In this article, we propose a multi-scale pipeline to allow automated classification of fish embryos (Medaka: Oryzias latipes) based on the presence or absence of spine malformations. The proposed pipeline relies on the acquisition of fish embryo 2D images, on feature extraction due to mathematical morphology operators and on machine learning classification. After image acquisition, segmentation tools are used to focus on the embryo before analysing several morphological features. An approach based on machine learning is then applied to these features to automatically classify embryos according to the detection of axial malformations. We built and validated our learning model on 1,459 images with a 10-fold cross- validation by comparison with the gold standard of 3D observations performed under a microscope by a trained operator. Our pipeline results in correct classification in 85% of the cases included in the database. This percentage is similar to the percentage of success of a trained human operator working on 2D images. Indeed, most of the errors are due to the inherent limitations of 2D images compared to 3D observations. The key benefit of our approach is the low computational cost of our image analysis pipeline, which guarantees optimal throughput analysis.

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Segmentation of gliomas and prediction of patient overall survival: A simple and fast procedure

Abstract

In this paper, we propose a fast automatic method that seg- ments glioma without any manual assistance, using a fully convolutional network (FCN) and transfer learning. From this segmentation, we predict the patient overall survival using only the results of the segmentation and a home made atlas. The FCN is the base network of VGG-16, pretrained on ImageNet for natural image classification, and fine tuned with the training dataset of the MICCAI 2018 BraTS Challenge. It relies on the “pseudo-3D” method published at ICIP 2017, which allows for segmenting objects from 2D color images which contain 3D information of MRI volumes. For each n th slice of the volume to segment, we consider three images, corresponding to the (n-1)th, nth, and (n-1)th slices of the original volume. These three gray-level 2D images are assembled to form a 2D RGB color image (one image per channel). This image is the input of the FCN to obtain a 2D segmentation of the n th slice. We process all slices, then stack the results to form the 3D output segmentation. With such a technique, the segmentation of a 3D volume takes only a few seconds. The prediction is based on Random Forests, and has the advantage of not being dependant of the acquisition modality, making it robust to inter-base data.

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Left atrial segmentation in a few seconds using fully convolutional network and transfer learning

Abstract

In this paper, we propose a fast automatic method that segments left atrial cavity from 3D GE-MRIs without any manual assistance, using a fully convolutional network (FCN) and transfer learning. This FCN is the base network of VGG-16, pre-trained on ImageNet for natural image classification, and fine tuned with the training dataset of the MICCAI 2018 Atrial Segmentation Challenge. It relies on the “pseudo-3D” method published at ICIP 2017, which allows for segmenting objects from 2D color images which contain 3D information of MRI volumes. For each $n^{\text{th}}$ slice of the volume to segment, we consider three images, corresponding to the $(n-1)^{\text{th}}$, $n^{\text{th}}$, and $(n+1)^{\text{th}}$ slices of the original volume. These three gray-level 2D images are assembled to form a 2D RGB color image (one image per channel). This image is the input of the FCN to obtain a 2D segmentation of the $n^{\text{th}}$ slice. We process all slices, then stack the results to form the 3D output segmentation. With such a technique, the segmentation of the left atrial cavity on a 3D volume takes only a few seconds. We obtain a Dice score of 0.92 both on the training set in our experiments before the challenge, and on the test set of the challenge.

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Real-time document detection in smartphone videos

Abstract

Smartphones are more and more used to capture photos of any kind of important documents in many different situations, yielding to new image processing needs. One of these is the ability of detecting documents in real time on smartphones’ video stream while being robust to classical defects such as low contrast, fuzzy images, flares, shadows, etc. This feature is interesting to help the user to capture his document in the best conditions and to guide this capture (evaluating appropriate distance, centering and tilt). In this paper we propose a solution to detect in real time documents taking very few assumptions concerning their contents and background. This method is based on morphological operators which contrasts with classical line detectors or gradient based thresholds. The use of such invariant operators makes our method robust to the defects encountered in video stream and suitable for real time document detection on smartphones.

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Segmentation des hyperintensités de la matière blanche en quelques secondes à l’aide d’un réseau de neurones convolutif et de transfert d’apprentissage

Abstract

Dans cet article, nous proposons une méthode automatique et rapide pour segmenter les hyper-intensités de la matière blanche (WMH) dans des images IRM cérébrales 3D, en utilisant un réseau de neurones entièrement convolutif (FCN) et du transfert d’apprentissage. Ce FCN est le réseau neuronal du Visual Geometry Group (VGG) pré-entraîné sur la base ImageNet pour la classification des images naturelles, et affiné avec l’ensemble des données d’entraînement du concours MICCAI WMH. Nous considérons trois images pour chaque coupe du volume à segmenter, provenant des acquisitions en T1, en FLAIR, et le résultat d’un opérateur morphologique appliqué sur le FLAIR, le top-hat, qui met en évidence les petites structures de forte intensité. Ces trois images 2D sont assemblées pour former une image 2D-3 canaux interprétée comme une image en couleurs, ensuite passée au FCN pour obtenir la segmentation 2D de la coupe correspondante. Nous traitons ainsi toutes les coupes pour former la segmentation de sortie 3D. Avec une telle technique, la segmentation de WMH sur un volume cérébral 3D prend environ 10 secondes, pré-traitement compris. Notre technique a été classée 6e sur 20 participants au concours MICCAI WMH.

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The challenge of cerebral magnetic resonance imaging in neonates: A new method using mathematical morphology for the segmentation of structures including diffuse excessive high signal intensities

Abstract

Preterm birth is a multifactorial condition associated with increased morbidity and mortality. Diffuse excessive high signal intensity (DEHSI) has been recently described on T2-weighted MR sequences in this population and thought to be associated with neuropathologies. To date, no robust and reproducible method to assess the presence of white matter hyperintensities has been developed, perhaps explaining the current controversy over their prognostic value. The aim of this paper is to propose a new semi-automated framework to detect DEHSI on neonatal brain MR images having a particular pattern due to the physiological lack of complete myelination of the white matter. A novel method for semi- automatic segmentation of neonatal brain structures and DEHSI, based on mathematical morphology and on max-tree representations of the images is thus described. It is a mandatory first step to identify and clinically assess homogeneous cohorts of neonates for DEHSI and/or volume of any other segmented structures. Implemented in a user-friendly interface, the method makes it straightforward to select relevant markers of structures to be segmented, and if needed, apply eventually manual corrections. This method responds to the increasing need for providing medical experts with semi-automatic tools for image analysis, and overcomes the limitations of visual analysis alone, prone to subjectivity and variability. Experimental results demonstrate that the method is accurate, with excellent reproducibility and with very few manual corrections needed. Although the method was intended initially for images acquired at 1.5T, which corresponds to usual clinical practice, preliminary results on images acquired at 3T suggest that the proposed approach can be generalized.

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White matter hyperintensities segmentation in a few seconds using fully convolutional network and transfer learning

Abstract

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A first step toward a fair comparison of evaluation protocols for text detection algorithms

Abstract

Text detection is an important topic in pattern recognition, but evaluating the reliability of such detection algorithms is challenging. While many evaluation protocols have been developed for that purpose, they often show dissimilar behaviors when applied in the same context. As a consequence, their usage may lead to misinterpretations, potentially yielding erroneous comparisons between detection algorithms or their incorrect parameters tuning. This paper is a first attempt to derive a methodology to perform the comparison of evaluation protocols. We then apply it on five state-of-the-art protocols, and exhibit that there indeed exist inconsistencies among their evaluation criteria. Our aim here is not to rank the investigated evaluation protocols, but rather raising awareness in the community that we should carefully reconsider them in order to converge to their optimal usage.

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Caractérisation des zones de mouvement périodiques pour applications bio-médicales

Abstract

De nombreuses applications biomedicales impliquent l’analyse de séquences pour la caractérisation du mouvement. Dans cet article, nous considerons des séquences 2D+t où un mouvement particulier (par exemple un flux sanguin) est associé à une zone spécifique de l’image 2D (par exemple une artère). Mais de nombreux mouvements peuvent co-exister dans les séquences (par exemple, il peut y avoir plusieurs vaisseaux sanguins presents, chacun avec leur flux spécifique). La caractérisation de ce type de mouvement implique d’abord de trouver les zones où le mouvement est présent, puis d’analyser ces mouvements : vitesse, régularité, fréquence, etc. Dans cet article, nous proposons une méthode appropriée pour détecter et caractériser simultanément les zones où le mouvement est présent dans une séquence. Nous pouvons ensuite classer ce mouvement en zones cohérentes en utilisant un apprentissage non supervisé et produire des métriques directement utilisables pour diverses applications. Nous illustrons et validons cette même méthode sur l’analyse du flux sanguin chez l’embryon de poisson.

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