Experimental digital gabor hologram rendering of C. Elegans worms by a model-trained convolutional neural network (conference presentation)
In Label-free biomedical imaging and sensing (LBIS) 2020
Learning endmember dynamics in multitemporal hyperspectral data using a state-space model formulation
In Proceedings of the 45th IEEE international conference on acoustics, speech, and signal processing (ICASSP)
Abstract
Hyperspectral image unmixing is an inverse problem aiming at recovering the spectral signatures of pure materials of interest (called endmembers) and estimating their proportions (called abundances) in every pixel of the image. However, in spite of a tremendous applicative potential and the avent of new satellite sensors with high temporal resolution, multitemporal hyperspectral unmixing is still a relatively underexplored research avenue in the community, compared to standard image unmixing. In this paper, we propose a new framework for multitemporal unmixing and endmember extraction based on a state-space model, and present a proof of concept on simulated data to show how this representation can be used to inform multitemporal unmixing with external prior knowledge, or on the contrary to learn the dynamics of the quantities involved from data using neural network architectures adapted to the identification of dynamical systems.
Braids of partitions for the hierarchical representation and segmentation of multimodal images
In Pattern Recognition
Abstract
Hierarchical data representations are powerful tools to analyze images and have found numerous applications in image processing. When it comes to multimodal images however, the fusion of multiple hierarchies remains an open question. Recently, the concept of braids of partitions has been proposed as a theoretical tool and possible solution to this issue. In this paper, we demonstrate the relevance of the braid structure for the hierarchical representation of multimodal images. We first propose a fully operable procedure to build a braid of partitions from two hierarchical representations. We then derive a framework for multimodal image segmentation, relying on an energetic minimization scheme conducted on the braid structure. The proposed approach is investigated on different multimodal images scenarios, and the obtained results confirm its ability to efficiently handle the multimodal information to produce more accurate segmentation outputs.
Estimation du niveau de bruit par arbre des formes et statistiques non paramétriques
In Proceedings of the 27st symposium on signal and image processing (GRETSI)
Abstract
La connaissance du niveau de bruit dans une image est précieuse pour de nombreuses applications en traitement d’images. L’estimation de la fonction de niveau de bruit requiert l’identification des zones homogènes sur lesquelles les paramètres du bruit peuvent être calculés. Sutour et al. en 2015 ont proposé une méthode d’estimation de la fonction de niveau de bruit se basant sur la recherche de zones homogènes de forme carrée, donc inadaptées au contenu local de l’image. Nous généralisons cette méthode à la recherche de zones homogènes de forme quelconque en nous basant sur la représentation par arbre des formes de l’image étudiée, permettant ainsi une estimation plus robuste de la fonction de niveau de bruit.
Estimating the noise level function with the tree of shapes and non-parametric statistics
In Proceedings of the 18th international conference on computer analysis of images and patterns (CAIP)
Abstract
The knowledge of the noise level within an image is a valuableinformation for many image processing applications. Estimating the noise level function (NLF) requires the identification of homogeneous regions, upon which the noise parameters are computed. Sutour et al. have proposed a method to estimate this NLF based on the search for homogeneous regions of square shape. We generalize this method to the search for homogeneous regions with arbitrary shape thanks to the tree of shapes representation of the image under study, thus allowing a more robust and precise estimation of the noise level function.
Constructing a braid of partitions from hierarchies of partitions
In Mathematical morphology and its application to signal and image processing – proceedings of the 14th international symposium on mathematical morphology (ISMM)
Abstract
Braids of partitions have been introduced in a theoretical framework as a generalization of hierarchies of partitions, but practical guidelines to derive such structures remained an open question. In a previous work, we proposed a methodology to build a braid of partitions by experimentally composing cuts extracted from two hierarchies of partitions, notably paving the way for the hierarchical representation of multimodal images. However, we did not provide the formal proof that our proposed methodology was yielding a braid structure. We remedy to this point in the present paper and give a brief insight on the structural properties of the resulting braid of partitions.
Motion compensation in digital holography for retinal imaging
In Proceedings of the IEEE international symposium on biomedical imaging (ISBI)
Abstract
The measurement of medical images can be hindered by blur and distortions caused by the physiological motion. Specially for retinal imaging, images are greatly affected by sharp movements of the eye. Stabilization methods have been developed and applied to state-of-the-art retinal imaging modalities; here we intend to adapt them for coherent light detection schemes. In this paper, we demonstrate experimentally cross-correlation-based lateral and axial motion compensation in laser Doppler imaging and optical coherence tomography by digital holography. Our methods improve lateral and axial image resolution in those innovative instruments and allow a better visualization during motion.
Segmentation of gliomas and prediction of patient overall survival: A simple and fast procedure
In Proceedings of the workshop on brain lesions (BrainLes), in conjunction with MICCAI
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.
Deep neural networks for aberrations compensation in digital holographic imaging of the retina
In Proceedings of the SPIE conference on adaptive optics and wavefront control for biological systems v
Abstract
In computational imaging by digital holography, lateral resolution of retinal images is limited to about 20 microns by the aberrations of the eye. To overcome this limitation, the aberrations have to be canceled. Digital aberration compensation can be performed by post-processing of full-field digital holograms. Aberration compensation was demonstrated from wavefront measurement by reconstruction of digital holograms in subapertures, and by measurement of a guide star hologram. Yet, these wavefront measurement methods have limited accuracy in practice. For holographic tomography of the human retina, image reconstruction was demonstrated by iterative digital aberration compensation, by minimization of the local entropy of speckle-averaged tomographic volumes. However image-based aberration compensation is time-consuming, preventing real-time image rendering. We are investigating a new digital aberration compensation scheme with a deep neural network to circumvent the limitations of these aberrations correction methods. To train the network, 28.000 anonymized images of eye fundus from patients of the 15-20 hospital in Paris have been collected, and synthetic interferograms have been reconstructed digitally by simulating the propagation of eye fundus images recorded with standard cameras. With a U-Net architecture, we demonstrate defocus correction of these complex-valued synthetic interferograms. Other aberration orders will be corrected with the same method, to improve lateral resolution up to the diffraction limit in digital holographic imaging of the retina.
A first step toward a fair comparison of evaluation protocols for text detection algorithms
In Proceedings of the IAPR international workshop on document analysis systems (DAS)
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.