Volume 4, Issue 1

Tissue clearing methods have boosted the microscopic observations of thick samples such as whole-mount mouse or zebrafish. Even with the best tissue clearing methods, specimens are not completely transparent and light attenuation increases with depth, reducing signal output and signal-to-noise ratio. In addition, since tissue clearing and microscopic acquisition techniques have become faster, automated image analysis is now an issue. In this context, mounting specimens at large scale often leads to imperfectly aligned or oriented samples, which makes relying on predefined, sample-independent parameters to correct signal attenuation impossible. Here, we propose a sample-dependent method for contrast correction. It relies on segmenting the sample, and estimating sample depth isosurfaces that serve as reference for the correction. We segment the brain white matter of zebrafish larvae. We show that this correction allows a better stitching of opposite sides of each larva, in order to image the entire larva with a high signal-to-noise ratio throughout. We also show that our proposed contrast correction method makes it possible to better recognize the deep structures of the brain by comparing manual vs. automated segmentations. This is expected to improve image observations and analyses in high-content methods where signal loss in the samples is significant.

Mathematical morphology is a powerful tool for image processing tasks. The main difficulty in designing mathematical morphological algorithm is deciding the order of operators/filters and the corresponding structuring elements (SEs). In this work, we develop morphological network composed of alternate sequences of dilation and erosion layers, which depending on learned SEs, may form opening or closing layers. These layers in the right order along with linear combination (of their outputs) are useful in extracting image features and processing them. Structuring elements in the network are learned by back-propagation method guided by minimization of the loss function. Efficacy of the proposed network is established by applying it to two interesting image restoration problems, namely de-raining and de-hazing . Results are comparable to that of many state-of-the-art algorithms for most of the images. It is also worth mentioning that the number of network parameters to handle is much less than that of popular convolutional neural network for similar tasks. The source code can be found here https://github.com/ranjanZ/Mophological-Opening-Closing-Net

Rhombic dodecahedron is a space filling polyhedron which represents the close packing of spheres in 3D space and the Voronoi structures of the face centered cubic (FCC) lattice. In this paper, we describe a new coordinate system where every 3-integer coordinates grid point corresponds to a rhombic dodecahedron centroid. In order to illustrate the interest of the new coordinate system, we propose the characterization of 3D digital plane with its topological features, such as the interrelation between the thickness of the digital plane and the separability constraint we aim to obtain. We also present the characterization of 3D digital lines and study it as the intersection of multiple digital planes. Characterization of 3D digital sphere with relevant topological features is proposed as well along with the 48-symmetry appearing in the new coordinate system.

This editorial presents the Special Issue dedicated to the conference ISMM 2019 and summarizes the articles published in this Special Issue.

Hyperspectral Image (HSI) classification refers to classifying hyperspectral data into features, where labels are given to pixels sharing the same features, distinguishing the present materials of the scene from one another. Naturally a HSI acquires spectral features of pixels, but spatial features based on neighborhood information are also important, which results in the problem of spectral-spatial classification. There are various ways to account to spatial information, one of which is through Mathematical Morphology, which is explored in this work. A HSI is a third-order data block, and building new spatial diversities may increase this order. In many cases, since pixel-wise classification requires a matrix of pixels and features, HSI data are reshaped as matrices which causes high dimensionality and ignores the multi-modal structure of the features. This work deals with HSI classification by modeling the data as tensors of high order. More precisely, multi-modal hyperspectral data is built and dealt with using tensor Canonical Polyadic (CP) decomposition. Experiments on real HSI show the effectiveness of the CP decomposition as a candidate for classification thanks to its properties of representing the pixel data in a matrix compact form with a low dimensional feature space while maintaining the multi-modality of the data.

When fitting archaeological artifacts, one would like to have a representation that simplifies fragments while preserving their complementarity. In this paper, we propose to employ the scale-spaces of mathematical morphology to hierarchically simplify potentially fitting fracture surfaces. We study the masking effect when morphological operations are applied to selected subsets of objects. Since fitting locally depends on the complementarity of fractures only, we introduce ‘Boundary Morphology’ on surfaces rather than volumes. Moreover, demonstrating the Lipschitz nature of the terracotta fractures informs our novel extrusion method to compute both closing and opening operations simultaneously. We also show that in this proposed representation the effects of abrasion and uncertainty are naturally bounded, justifying the morphological approach. This work is an extension of our contribution earlier published in the proceedings of ISMM2019 [10].

This paper addresses the issue of building a part-based representation of a dataset of images. More precisely, we look for a non-negative, sparse decomposition of the images on a reduced set of atoms, in order to unveil a morphological and explainable structure of the data. Additionally, we want this decomposition to be computed online for any new sample that is not part of the initial dataset. Therefore, our solution relies on a sparse, non-negative auto-encoder, where the encoder is deep (for accuracy) and the decoder shallow (for explainability). This method compares favorably to the state-of-the-art online methods on two benchmark datasets (MNIST and Fashion MNIST) and on a hyperspectral image, according to classical evaluation measures and to a new one we introduce, based on the equivariance of the representation to morphological operators.

This paper proposes a way of better approximating continuous, two-dimensional morphology in the discrete domain, by allowing for irregularly sampled input and output signals. We generalize previous work to allow for a greater variety of structuring elements, both flat and non-flat. Experimentally we show improved results over regular, discrete morphology with respect to the approximation of continuous morphology. It is also worth noting that the number of output samples can often be reduced without sacrificing the quality of the approximation, since the morphological operators usually generate output signals with many plateaus, which, intuitively do not need a large number of samples to be correctly represented. Finally, the paper presents some results showing adaptive morphology on irregularly sampled signals.

In this article, we present a fast-marching based algorithm for generating superpixel (FMS) partitions of images. The idea behind the algorithm is to draw an analogy between waves propagating in a heterogeneous medium and regions growing on an image at a rate depending on the local color and texture. The FMS algorithm is evaluated on the Berkeley Segmentation Dataset 500. It yields results in terms of boundary adherence that are slightly better than the ones obtained with similar approaches including the Simple Linear Iterative Clustering, the Eikonal-based region growing for efficient clustering and the Iterative Spanning Forest framework for superpixel segmentation algorithms. An interesting feature of the proposed algorithm is that it can take into account texture information to compute the superpixel partition. We illustrate the interest of adding texture information on a specific set of images obtained by recombining textures patches extracted from images representing stripes, originally constructed by Giraud et al. [20]. On this dataset, our approach works significantly better than color based superpixel algorithms.