Grey-scale 1-D dilations with spatially-variant structuring elements in linear time

Full text also available online for free at http://www.eurasip.org/Proceedings/Eusipco/Eusipco2008/International audienceSpatially variant morphological operators can significantly improve filtering capabilities or object detection score of various applications. Whereas an effort has been made to define the theoretical background, the efficient implementation of adaptable algorithms remained far less considered. In this paper, we present an efficient,one-scan, linear algorithm for 1-D grey-scale dilations/erosions with spatially variant structuring elements. The proposed algorithm processes data in stream, can work in place and produces results with minimal latency. The computing time is independent of the structuring element size

Direction-adaptive grey-level morphology. Application to 3D vascular brain imaging

International audienceSegmentation and analysis of blood vessels is an important issue in medical imaging. In 3D cerebral angiographic data, the vascular signal is however hard to accurately detect and can, in particular, be disconnected. In this article, we present a procedure utilising both linear, Hessian-based and morphological methods for blood vessel edge enhancement and reconnection. More specifically, multi-scale second-order derivative analysis is performed to detect candidate vessels as well as their orientation. This information is then fed to a spatially-variant morphological filter for reconnection and reconstruction. The result is a fast and effective vessel-reconnecting method

Computationally efficient, one-pass algorithm for morphological filters

International audienceMany useful morphological filters are built as long concatenations of erosions and dilations: openings, closings, size distributions, sequential filters, etc. This paper proposes a new algorithm implementing morphological dilation and erosion of functions. It supports rectangular structuring element, runs in linear time w.r.t. the image size and constant time w.r.t. the structuring element size, and has minimal memory usage. It has zero algorithm latency and processes data in stream. These properties are inherited by operators composed by concatenation, and allow their efficient implementation. We show how to compute in one pass an Alternate Sequential Filter (ASF(n)) regardless the number of stages n. This algorithm opens the way to such time-critical applications where the complexity and memory requirements of serial morphological operators represented a bottleneck limiting their usability. (C) 2011 Elsevier Inc. All rights reserved

Spatially resolved clonal copy number alterations in benign and malignant tissue

Publisher Copyright: © 2022, The Author(s).Defining the transition from benign to malignant tissue is fundamental to improving early diagnosis of cancer1. Here we use a systematic approach to study spatial genome integrity in situ and describe previously unidentified clonal relationships. We used spatially resolved transcriptomics2 to infer spatial copy number variations in >120,000 regions across multiple organs, in benign and malignant tissues. We demonstrate that genome-wide copy number variation reveals distinct clonal patterns within tumours and in nearby benign tissue using an organ-wide approach focused on the prostate. Our results suggest a model for how genomic instability arises in histologically benign tissue that may represent early events in cancer evolution. We highlight the power of capturing the molecular and spatial continuums in a tissue context and challenge the rationale for treatment paradigms, including focal therapy.Peer reviewe

Spatially resolved clonal copy number alterations in benign and malignant tissue

Publisher Copyright: © 2022, The Author(s).Defining the transition from benign to malignant tissue is fundamental to improving early diagnosis of cancer1. Here we use a systematic approach to study spatial genome integrity in situ and describe previously unidentified clonal relationships. We used spatially resolved transcriptomics2 to infer spatial copy number variations in >120,000 regions across multiple organs, in benign and malignant tissues. We demonstrate that genome-wide copy number variation reveals distinct clonal patterns within tumours and in nearby benign tissue using an organ-wide approach focused on the prostate. Our results suggest a model for how genomic instability arises in histologically benign tissue that may represent early events in cancer evolution. We highlight the power of capturing the molecular and spatial continuums in a tissue context and challenge the rationale for treatment paradigms, including focal therapy.Peer reviewe

Alongshore coupling of eco-geomorphological variables in a beach-dune system

ABSTRACT: Coastal dune systems are becoming increasingly vulnerable to erosion and washover due to sea-level rise and changes in storm activity with changing climate. The impact, however, is not consistent within and across coastal barriers and there is a need to examine the alongshore variability of beach-dune systems to understand dune resiliency. This includes vegetation, which is responsible for trapping transported sediment and initiating dune formation and varies alongshore in response to a poorly understood eco-geomorphological feedback. Identifying how beach-dune systems and vegetation vary alongshore is important for understanding their resiliency. In previous studies it has been suggested that this feedback leads to scale-invariant foredunes in which the maximum potential dune height is directly related to the distance between vegetation and the shoreline (Lveg). There is, however, no corresponding field data to support this model result across and within barrier systems. This study involves the collection of field data from three beaches along the North Shore of Prince Edward Island, Canada. The dune systems are primarily vegetated by Ammophila breviligulata and vegetation density ranged from 0% to 100% beyond the dune crest, with considerable variability alongshore and between sites. The alongshore variability of the vegetation and its relationship to the morphology of the dune was examined using a 1x1m digital elevation model generated from Structure for Motion using Unoccupied Aerial Vehicles and LiDAR topobathy collected by CBCL Limited. Results suggest that dune morphology is not scale-invariant and that the relationship between dune height and vegetation is dependent on storm surge and beach envelope limits to the establishment of vegetation. Comparison to previously published data from a range of sites supports the scale-variant relationship identified in this study and suggest the need to consider development as a combination of transport, supply, and history

Bayesian Modelling of Induced Responses and Neuronal Rhythms

Neural rhythms or oscillations are ubiquitous in neuroimaging data. These spectral responses have been linked to several cognitive processes; including working memory, attention, perceptual binding and neuronal coordination. In this paper, we show how Bayesian methods can be used to finesse the ill-posed problem of reconstructing-and explaining-oscillatory responses. We offer an overview of recent developments in this field, focusing on (i) the use of MEG data and Empirical Bayes to build hierarchical models for group analyses-and the identification of important sources of inter-subject variability and (ii) the construction of novel dynamic causal models of intralaminar recordings to explain layer-specific activity. We hope to show that electrophysiological measurements contain much more spatial information than is often thought: on the one hand, the dynamic causal modelling of non-invasive (low spatial resolution) electrophysiology can afford sub-millimetre (hyper-acute) resolution that is limited only by the (spatial) complexity of the underlying (dynamic causal) forward model. On the other hand, invasive microelectrode recordings (that penetrate different cortical layers) can reveal laminar-specific responses and elucidate hierarchical message passing and information processing within and between cortical regions at a macroscopic scale. In short, the careful and biophysically grounded modelling of sparse data enables one to characterise the neuronal architectures generating oscillations in a remarkable detail

Remote refocusing light-sheet fluorescence microscopy for high-speed 2D and 3D imaging of calcium dynamics in cardiomyocytes

The high prevalence and poor prognosis of heart failure are two key drivers for research into cardiac electrophysiology and regeneration. Dyssynchrony in calcium release and loss of structural organization within individual cardiomyocytes (CM) has been linked to reduced contractile strength and arrhythmia. Correlating calcium dynamics and cell microstructure requires multidimensional imaging with high spatiotemporal resolution. In light-sheet fluorescence microscopy (LSFM), selective plane illumination enables fast optically sectioned imaging with lower phototoxicity, making it suitable for imaging subcellular dynamics. In this work, a custom remote refocusing LSFM system is applied to studying calcium dynamics in isolated CM, cardiac cell cultures and tissue slices. The spatial resolution of the LSFM system was modelled and experimentally characterized. Simulation of the illumination path in Zemax was used to estimate the light-sheet beam waist and confocal parameter. Automated MATLAB-based image analysis was used to quantify the optical sectioning and the 3D point spread function using Gaussian fitting of bead image intensity distributions. The results demonstrated improved and more uniform axial resolution and optical sectioning with the tighter focused beam used for axially swept light-sheet microscopy. High-speed dual-channel LSFM was used for 2D imaging of calcium dynamics in correlation with the t-tubule structure in left and right ventricle cardiomyocytes at 395 fps. The high spatio-temporal resolution enabled the characterization of calcium sparks. The use of para-nitro-blebbistatin (NBleb), a non-phototoxic, low fluorescence contraction uncoupler, allowed 2D-mapping of the spatial dyssynchrony of calcium transient development across the cell. Finally, aberration-free remote refocusing was used for high-speed volumetric imaging of calcium dynamics in human induced pluripotent stem-cell derived cardiomyocytes (hiPSC-CM) and their co-culture with adult-CM. 3D-imaging at up to 8 Hz demonstrated the synchronization of calcium transients in co-culture, with increased coupling with longer co-culture duration, uninhibited by motion uncoupling with NBleb.Open Acces