arXiv subjects

Pierre-Henri Conze

Publications and source records attributed to Pierre-Henri Conze.

At least 37 records · Page 2Linked to original sources

arXiv2023

Cross-dimensional transfer learning in medical image segmentation with deep learning

Over the last decade, convolutional neural networks have emerged and advanced the state-of-the-art in various image analysis and computer vision applications. The performance of 2D image classification networks is constantly improving and being trained on databases made of millions of natural images. However, progress in medical image analysis has been hindered by limited annotated data and acquisition constraints. These limitations are even more pronounced given the volumetry of medical imaging data. In this paper, we introduce an efficient way to transfer the efficiency of a 2D classification network trained on natural images to 2D, 3D uni- and multi-modal medical image segmentation applications. In this direction, we designed novel architectures based on two key principles: weight transfer by embedding a 2D pre-trained encoder into a higher dimensional U-Net, and dimensional transfer by expanding a 2D segmentation network into a higher dimension one. The proposed networks were tested on benchmarks comprising different modalities: MR, CT, and ultrasound images. Our 2D network ranked first on the CAMUS challenge dedicated to echo-cardiographic data segmentation and surpassed the state-of-the-art. Regarding 2D/3D MR and CT abdominal images from the CHAOS challenge, our approach largely outperformed the other 2D-based methods described in the challenge paper on Dice, RAVD, ASSD, and MSSD scores and ranked third on the online evaluation platform. Our 3D network applied to the BraTS 2022 competition also achieved promising results, reaching an average Dice score of 91.69% (91.22%) for the whole tumor, 83.23% (84.77%) for the tumor core, and 81.75% (83.88%) for enhanced tumor using the approach based on weight (dimensional) transfer. Experimental and qualitative results illustrate the effectiveness of our methods for multi-dimensional medical image segmentation.

eess.IV↗

arXiv2023

Multimodal Information Fusion For The Diagnosis Of Diabetic Retinopathy

Diabetes is a chronic disease characterized by excess sugar in the blood and affects 422 million people worldwide, including 3.3 million in France. One of the frequent complications of diabetes is diabetic retinopathy (DR): it is the leading cause of blindness in the working population of developed countries. As a result, ophthalmology is on the verge of a revolution in screening, diagnosing, and managing of pathologies. This upheaval is led by the arrival of technologies based on artificial intelligence. The "Evaluation intelligente de la rétinopathie diabétique" (EviRed) project uses artificial intelligence to answer a medical need: replacing the current classification of diabetic retinopathy which is mainly based on outdated fundus photography and providing an insufficient prediction precision. EviRed exploits modern fundus imaging devices and artificial intelligence to properly integrate the vast amount of data they provide with other available medical data of the patient. The goal is to improve diagnosis and prediction and help ophthalmologists to make better decisions during diabetic retinopathy follow-up. In this study, we investigate the fusion of different modalities acquired simultaneously with a PLEXElite 9000 (Carl Zeiss Meditec Inc. Dublin, California, USA), namely 3-D structural optical coherence tomography (OCT), 3-D OCT angiography (OCTA) and 2-D Line Scanning Ophthalmoscope (LSO), for the automatic detection of proliferative DR.

eess.IV↗

arXiv2022

Segmentation, Classification, and Quality Assessment of UW-OCTA Images for the Diagnosis of Diabetic Retinopathy

Diabetic Retinopathy (DR) is a severe complication of diabetes that can cause blindness. Although effective treatments exist (notably laser) to slow the progression of the disease and prevent blindness, the best treatment remains prevention through regular check-ups (at least once a year) with an ophthalmologist. Optical Coherence Tomography Angiography (OCTA) allows for the visualization of the retinal vascularization, and the choroid at the microvascular level in great detail. This allows doctors to diagnose DR with more precision. In recent years, algorithms for DR diagnosis have emerged along with the development of deep learning and the improvement of computer hardware. However, these usually focus on retina photography. There are no current methods that can automatically analyze DR using Ultra-Wide OCTA (UW-OCTA). The Diabetic Retinopathy Analysis Challenge 2022 (DRAC22) provides a standardized UW-OCTA dataset to train and test the effectiveness of various algorithms on three tasks: lesions segmentation, quality assessment, and DR grading. In this paper, we will present our solutions for the three tasks of the DRAC22 challenge. The obtained results are promising and have allowed us to position ourselves in the TOP 5 of the segmentation task, the TOP 4 of the quality assessment task, and the TOP 3 of the DR grading task. The code is available at \url{https://github.com/Mostafa-EHD/Diabetic_Retinopathy_OCTA}.

eess.IV↗

arXiv2022

Multimodal Information Fusion for Glaucoma and DR Classification

Multimodal information is frequently available in medical tasks. By combining information from multiple sources, clinicians are able to make more accurate judgments. In recent years, multiple imaging techniques have been used in clinical practice for retinal analysis: 2D fundus photographs, 3D optical coherence tomography (OCT) and 3D OCT angiography, etc. Our paper investigates three multimodal information fusion strategies based on deep learning to solve retinal analysis tasks: early fusion, intermediate fusion, and hierarchical fusion. The commonly used early and intermediate fusions are simple but do not fully exploit the complementary information between modalities. We developed a hierarchical fusion approach that focuses on combining features across multiple dimensions of the network, as well as exploring the correlation between modalities. These approaches were applied to glaucoma and diabetic retinopathy classification, using the public GAMMA dataset (fundus photographs and OCT) and a private dataset of PlexElite 9000 (Carl Zeis Meditec Inc.) OCT angiography acquisitions, respectively. Our hierarchical fusion method performed the best in both cases and paved the way for better clinical diagnosis.

eess.IV↗

arXiv2022

Mapping the ocular surface from monocular videos with an application to dry eye disease grading

With a prevalence of 5 to 50%, Dry Eye Disease (DED) is one of the leading reasons for ophthalmologist consultations. The diagnosis and quantification of DED usually rely on ocular surface analysis through slit-lamp examinations. However, evaluations are subjective and non-reproducible. To improve the diagnosis, we propose to 1) track the ocular surface in 3-D using video recordings acquired during examinations, and 2) grade the severity using registered frames. Our registration method uses unsupervised image-to-depth learning. These methods learn depth from lights and shadows and estimate pose based on depth maps. However, DED examinations undergo unresolved challenges including a moving light source, transparent ocular tissues, etc. To overcome these and estimate the ego-motion, we implement joint CNN architectures with multiple losses incorporating prior known information, namely the shape of the eye, through semantic segmentation as well as sphere fitting. The achieved tracking errors outperform the state-of-the-art, with a mean Euclidean distance as low as 0.48% of the image width on our test set. This registration improves the DED severity classification by a 0.20 AUC difference. The proposed approach is the first to address DED diagnosis with supervision from monocular videos

cs.CV↗

arXiv2022

Generalizable multi-task, multi-domain deep segmentation of sparse pediatric imaging datasets via multi-scale contrastive regularization and multi-joint anatomical priors

Clinical diagnosis of the pediatric musculoskeletal system relies on the analysis of medical imaging examinations. In the medical image processing pipeline, semantic segmentation using deep learning algorithms enables an automatic generation of patient-specific three-dimensional anatomical models which are crucial for morphological evaluation. However, the scarcity of pediatric imaging resources may result in reduced accuracy and generalization performance of individual deep segmentation models. In this study, we propose to design a novel multi-task, multi-domain learning framework in which a single segmentation network is optimized over the union of multiple datasets arising from distinct parts of the anatomy. Unlike previous approaches, we simultaneously consider multiple intensity domains and segmentation tasks to overcome the inherent scarcity of pediatric data while leveraging shared features between imaging datasets. To further improve generalization capabilities, we employ a transfer learning scheme from natural image classification, along with a multi-scale contrastive regularization aimed at promoting domain-specific clusters in the shared representations, and multi-joint anatomical priors to enforce anatomically consistent predictions. We evaluate our contributions for performing bone segmentation using three scarce and pediatric imaging datasets of the ankle, knee, and shoulder joints. Our results demonstrate that the proposed approach outperforms individual, transfer, and shared segmentation schemes in Dice metric with statistically sufficient margins. The proposed model brings new perspectives towards intelligent use of imaging resources and better management of pediatric musculoskeletal disorders.

eess.IV↗

arXiv2022

Multi-structure bone segmentation in pediatric MR images with combined regularization from shape priors and adversarial network

Morphological and diagnostic evaluation of pediatric musculoskeletal system is crucial in clinical practice. However, most segmentation models do not perform well on scarce pediatric imaging data. We propose a new pre-trained regularized convolutional encoder-decoder network for the challenging task of segmenting heterogeneous pediatric magnetic resonance (MR) images. To this end, we have conceived a novel optimization scheme for the segmentation network which comprises additional regularization terms to the loss function. In order to obtain globally consistent predictions, we incorporate a shape priors based regularization, derived from a non-linear shape representation learnt by an auto-encoder. Additionally, an adversarial regularization computed by a discriminator is integrated to encourage precise delineations. The proposed method is evaluated for the task of multi-bone segmentation on two scarce pediatric imaging datasets from ankle and shoulder joints, comprising pathological as well as healthy examinations. The proposed method performed either better or at par with previously proposed approaches for Dice, sensitivity, specificity, maximum symmetric surface distance, average symmetric surface distance, and relative absolute volume difference metrics. We illustrate that the proposed approach can be easily integrated into various bone segmentation strategies and can improve the prediction accuracy of models pre-trained on large non-medical images databases. The obtained results bring new perspectives for the management of pediatric musculoskeletal disorders.

eess.IV↗

arXiv2022

Multi-Task, Multi-Domain Deep Segmentation with Shared Representations and Contrastive Regularization for Sparse Pediatric Datasets

Automatic segmentation of magnetic resonance (MR) images is crucial for morphological evaluation of the pediatric musculoskeletal system in clinical practice. However, the accuracy and generalization performance of individual segmentation models are limited due to the restricted amount of annotated pediatric data. Hence, we propose to train a segmentation model on multiple datasets, arising from different parts of the anatomy, in a multi-task and multi-domain learning framework. This approach allows to overcome the inherent scarcity of pediatric data while benefiting from a more robust shared representation. The proposed segmentation network comprises shared convolutional filters, domain-specific batch normalization parameters that compute the respective dataset statistics and a domain-specific segmentation layer. Furthermore, a supervised contrastive regularization is integrated to further improve generalization capabilities, by promoting intra-domain similarity and impose inter-domain margins in embedded space. We evaluate our contributions on two pediatric imaging datasets of the ankle and shoulder joints for bone segmentation. Results demonstrate that the proposed model outperforms state-of-the-art approaches.

cs.CV↗

arXiv2021

Regularized directional representations for medical image registration

In image registration, many efforts have been devoted to the development of alternatives to the popular normalized mutual information criterion. Concurrently to these efforts, an increasing number of works have demonstrated that substantial gains in registration accuracy can also be achieved by aligning structural representations of images rather than images themselves. Following this research path, we propose a new method for mono- and multimodal image registration based on the alignment of regularized vector fields derived from structural information such as gradient vector flow fields, a technique we call \textit{vector field similarity}. Our approach can be combined in a straightforward fashion with any existing registration framework by substituting vector field similarity to intensity-based registration. In our experiments, we show that the proposed approach compares favourably with conventional image alignment on several public image datasets using a diversity of imaging modalities and anatomical locations.

cs.CV↗

arXiv2021

ExplAIn: Explanatory Artificial Intelligence for Diabetic Retinopathy Diagnosis

In recent years, Artificial Intelligence (AI) has proven its relevance for medical decision support. However, the "black-box" nature of successful AI algorithms still holds back their wide-spread deployment. In this paper, we describe an eXplanatory Artificial Intelligence (XAI) that reaches the same level of performance as black-box AI, for the task of classifying Diabetic Retinopathy (DR) severity using Color Fundus Photography (CFP). This algorithm, called ExplAIn, learns to segment and categorize lesions in images; the final image-level classification directly derives from these multivariate lesion segmentations. The novelty of this explanatory framework is that it is trained from end to end, with image supervision only, just like black-box AI algorithms: the concepts of lesions and lesion categories emerge by themselves. For improved lesion localization, foreground/background separation is trained through self-supervision, in such a way that occluding foreground pixels transforms the input image into a healthy-looking image. The advantage of such an architecture is that automatic diagnoses can be explained simply by an image and/or a few sentences. ExplAIn is evaluated at the image level and at the pixel level on various CFP image datasets. We expect this new framework, which jointly offers high classification performance and explainability, to facilitate AI deployment.

cs.CV↗

arXiv2021

Multi-Structure Deep Segmentation with Shape Priors and Latent Adversarial Regularization

Automatic segmentation of the musculoskeletal system in pediatric magnetic resonance (MR) images is a challenging but crucial task for morphological evaluation in clinical practice. We propose a deep learning-based regularized segmentation method for multi-structure bone delineation in MR images, designed to overcome the inherent scarcity and heterogeneity of pediatric data. Based on a newly devised shape code discriminator, our adversarial regularization scheme enforces the deep network to follow a learnt shape representation of the anatomy. The novel shape priors based adversarial regularization (SPAR) exploits latent shape codes arising from ground truth and predicted masks to guide the segmentation network towards more consistent and plausible predictions. Our contribution is compared to state-of-the-art regularization methods on two pediatric musculoskeletal imaging datasets from ankle and shoulder joints.

eess.IV↗

arXiv2021

CHAOS Challenge -- Combined (CT-MR) Healthy Abdominal Organ Segmentation

Segmentation of abdominal organs has been a comprehensive, yet unresolved, research field for many years. In the last decade, intensive developments in deep learning (DL) have introduced new state-of-the-art segmentation systems. In order to expand the knowledge on these topics, the CHAOS - Combined (CT-MR) Healthy Abdominal Organ Segmentation challenge has been organized in conjunction with IEEE International Symposium on Biomedical Imaging (ISBI), 2019, in Venice, Italy. CHAOS provides both abdominal CT and MR data from healthy subjects for single and multiple abdominal organ segmentation. Five different but complementary tasks have been designed to analyze the capabilities of current approaches from multiple perspectives. The results are investigated thoroughly, compared with manual annotations and interactive methods. The analysis shows that the performance of DL models for single modality (CT / MR) can show reliable volumetric analysis performance (DICE: 0.98 $\pm$ 0.00 / 0.95 $\pm$ 0.01) but the best MSSD performance remain limited (21.89 $\pm$ 13.94 / 20.85 $\pm$ 10.63 mm). The performances of participating models decrease significantly for cross-modality tasks for the liver (DICE: 0.88 $\pm$ 0.15 MSSD: 36.33 $\pm$ 21.97 mm) and all organs (DICE: 0.85 $\pm$ 0.21 MSSD: 33.17 $\pm$ 38.93 mm). Despite contrary examples on different applications, multi-tasking DL models designed to segment all organs seem to perform worse compared to organ-specific ones (performance drop around 5\%). Besides, such directions of further research for cross-modality segmentation would significantly support real-world clinical applications. Moreover, having more than 1500 participants, another important contribution of the paper is the analysis on shortcomings of challenge organizations such as the effects of multiple submissions and peeking phenomena.

eess.IV↗

arXiv2020

Two-stage multi-scale breast mass segmentation for full mammogram analysis without user intervention

Mammography is the primary imaging modality used for early detection and diagnosis of breast cancer. X-ray mammogram analysis mainly refers to the localization of suspicious regions of interest followed by segmentation, towards further lesion classification into benign versus malignant. Among diverse types of breast abnormalities, masses are the most important clinical findings of breast carcinomas. However, manually segmenting breast masses from native mammograms is time-consuming and error-prone. Therefore, an integrated computer-aided diagnosis system is required to assist clinicians for automatic and precise breast mass delineation. In this work, we present a two-stage multi-scale pipeline that provides accurate mass contours from high-resolution full mammograms. First, we propose an extended deep detector integrating a multi-scale fusion strategy for automated mass localization. Second, a convolutional encoder-decoder network using nested and dense skip connections is employed to fine-delineate candidate masses. Unlike most previous studies based on segmentation from regions, our framework handles mass segmentation from native full mammograms without any user intervention. Trained on INbreast and DDSM-CBIS public datasets, the pipeline achieves an overall average Dice of 80.44% on INbreast test images, outperforming state-of-the-art. Our system shows promising accuracy as an automatic full-image mass segmentation system. Extensive experiments reveals robustness against the diversity of size, shape and appearance of breast masses, towards better interaction-free computer-aided diagnosis.

eess.IV↗

arXiv2020

Efficient embedding network for 3D brain tumor segmentation

3D medical image processing with deep learning greatly suffers from a lack of data. Thus, studies carried out in this field are limited compared to works related to 2D natural image analysis, where very large datasets exist. As a result, powerful and efficient 2D convolutional neural networks have been developed and trained. In this paper, we investigate a way to transfer the performance of a two-dimensional classiffication network for the purpose of three-dimensional semantic segmentation of brain tumors. We propose an asymmetric U-Net network by incorporating the EfficientNet model as part of the encoding branch. As the input data is in 3D, the first layers of the encoder are devoted to the reduction of the third dimension in order to fit the input of the EfficientNet network. Experimental results on validation and test data from the BraTS 2020 challenge demonstrate that the proposed method achieve promising performance.

cs.CV↗

arXiv2020

Healthy versus pathological learning transferability in shoulder muscle MRI segmentation using deep convolutional encoder-decoders

Automatic segmentation of pathological shoulder muscles in patients with musculo-skeletal diseases is a challenging task due to the huge variability in muscle shape, size, location, texture and injury. A reliable fully-automated segmentation method from magnetic resonance images could greatly help clinicians to plan therapeutic interventions and predict interventional outcomes while eliminating time consuming manual segmentation efforts. The purpose of this work is three-fold. First, we investigate the feasibility of pathological shoulder muscle segmentation using deep learning techniques, given a very limited amount of available annotated pediatric data. Second, we address the learning transferability from healthy to pathological data by comparing different learning schemes in terms of model generalizability. Third, extended versions of deep convolutional encoder-decoder architectures using encoders pre-trained on non-medical data are proposed to improve the segmentation accuracy. Methodological aspects are evaluated in a leave-one-out fashion on a dataset of 24 shoulder examinations from patients with obstetrical brachial plexus palsy and focus on 4 different muscles including deltoid as well as infraspinatus, supraspinatus and subscapularis from the rotator cuff. The most relevant segmentation model is partially pre-trained on ImageNet and jointly exploits inter-patient healthy and pathological annotated data. Its performance reaches Dice scores of 82.4%, 82.0%, 71.0% and 82.8% for deltoid, infraspinatus, supraspinatus and subscapularis muscles. Absolute surface estimation errors are all below 83mm$^2$ except for supraspinatus with 134.6mm$^2$. These contributions offer new perspectives for force inference in the context of musculo-skeletal disorder management.

cs.CV↗

arXiv2020

Automatic detection of rare pathologies in fundus photographs using few-shot learning

In the last decades, large datasets of fundus photographs have been collected in diabetic retinopathy (DR) screening networks. Through deep learning, these datasets were used to train automatic detectors for DR and a few other frequent pathologies, with the goal to automate screening. One challenge limits the adoption of such systems so far: automatic detectors ignore rare conditions that ophthalmologists currently detect, such as papilledema or anterior ischemic optic neuropathy. The reason is that standard deep learning requires too many examples of these conditions. However, this limitation can be addressed with few-shot learning, a machine learning paradigm where a classifier has to generalize to a new category not seen in training, given only a few examples of this category. This paper presents a new few-shot learning framework that extends convolutional neural networks (CNNs), trained for frequent conditions, with an unsupervised probabilistic model for rare condition detection. It is based on the observation that CNNs often perceive photographs containing the same anomalies as similar, even though these CNNs were trained to detect unrelated conditions. This observation was based on the t-SNE visualization tool, which we decided to incorporate in our probabilistic model. Experiments on a dataset of 164,660 screening examinations from the OPHDIAT screening network show that 37 conditions, out of 41, can be detected with an area under the ROC curve (AUC) greater than 0.8 (average AUC: 0.938). In particular, this framework significantly outperforms other frameworks for detecting rare conditions, including multitask learning, transfer learning and Siamese networks, another few-shot learning solution. We expect these richer predictions to trigger the adoption of automated eye pathology screening, which will revolutionize clinical practice in ophthalmology.

cs.CV↗

arXiv2020

Abdominal multi-organ segmentation with cascaded convolutional and adversarial deep networks

Objective : Abdominal anatomy segmentation is crucial for numerous applications from computer-assisted diagnosis to image-guided surgery. In this context, we address fully-automated multi-organ segmentation from abdominal CT and MR images using deep learning. Methods: The proposed model extends standard conditional generative adversarial networks. Additionally to the discriminator which enforces the model to create realistic organ delineations, it embeds cascaded partially pre-trained convolutional encoder-decoders as generator. Encoder fine-tuning from a large amount of non-medical images alleviates data scarcity limitations. The network is trained end-to-end to benefit from simultaneous multi-level segmentation refinements using auto-context. Results : Employed for healthy liver, kidneys and spleen segmentation, our pipeline provides promising results by outperforming state-of-the-art encoder-decoder schemes. Followed for the Combined Healthy Abdominal Organ Segmentation (CHAOS) challenge organized in conjunction with the IEEE International Symposium on Biomedical Imaging 2019, it gave us the first rank for three competition categories: liver CT, liver MR and multi-organ MR segmentation. Conclusion : Combining cascaded convolutional and adversarial networks strengthens the ability of deep learning pipelines to automatically delineate multiple abdominal organs, with good generalization capability. Significance : The comprehensive evaluation provided suggests that better guidance could be achieved to help clinicians in abdominal image interpretation and clinical decision making.

eess.IV↗

arXiv2020

Combining Shape Priors with Conditional Adversarial Networks for Improved Scapula Segmentation in MR images

This paper proposes an automatic method for scapula bone segmentation from Magnetic Resonance (MR) images using deep learning. The purpose of this work is to incorporate anatomical priors into a conditional adversarial framework, given a limited amount of heterogeneous annotated images. Our approach encourages the segmentation model to follow the global anatomical properties of the underlying anatomy through a learnt non-linear shape representation while the adversarial contribution refines the model by promoting realistic delineations. These contributions are evaluated on a dataset of 15 pediatric shoulder examinations, and compared to state-of-the-art architectures including UNet and recent derivatives. The significant improvements achieved bring new perspectives for the pre-operative management of musculo-skeletal diseases.

eess.IV↗