On The Continuous Steering of the Scale of Tight Wavelet Frames

In analogy with steerable wavelets, we present a general construction of adaptable tight wavelet frames, with an emphasis on scaling operations. In particular, the derived wavelets can be "dilated" by a procedure comparable to the operation of steering steerable wavelets. The fundamental aspects of the construction are the same: an admissible collection of Fourier multipliers is used to extend a tight wavelet frame, and the "scale" of the wavelets is adapted by scaling the multipliers. As an application, the proposed wavelets can be used to improve the frequency localization. Importantly, the localized frequency bands specified by this construction can be scaled efficiently using matrix multiplication

Particle detection and tracking in fluorescence time-lapse imaging: a contrario approach

This paper proposes a probabilistic approach for the detection and the tracking of particles in fluorescent time-lapse imaging. In the presence of a very noised and poor-quality data, particles and trajectories can be characterized by an a contrario model, that estimates the probability of observing the structures of interest in random data. This approach, first introduced in the modeling of human visual perception and then successfully applied in many image processing tasks, leads to algorithms that neither require a previous learning stage, nor a tedious parameter tuning and are very robust to noise. Comparative evaluations against a well-established baseline show that the proposed approach outperforms the state of the art.Comment: Published in Journal of Machine Vision and Application

Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images

<p>Abstract</p> <p>Background</p> <p>Several algorithms have been proposed for detecting fluorescently labeled subcellular objects in microscope images. Many of these algorithms have been designed for specific tasks and validated with limited image data. But despite the potential of using extensive comparisons between algorithms to provide useful information to guide method selection and thus more accurate results, relatively few studies have been performed.</p> <p>Results</p> <p>To better understand algorithm performance under different conditions, we have carried out a comparative study including eleven spot detection or segmentation algorithms from various application fields. We used microscope images from well plate experiments with a human osteosarcoma cell line and frames from image stacks of yeast cells in different focal planes. These experimentally derived images permit a comparison of method performance in realistic situations where the number of objects varies within image set. We also used simulated microscope images in order to compare the methods and validate them against a ground truth reference result. Our study finds major differences in the performance of different algorithms, in terms of both object counts and segmentation accuracies.</p> <p>Conclusions</p> <p>These results suggest that the selection of detection algorithms for image based screens should be done carefully and take into account different conditions, such as the possibility of acquiring empty images or images with very few spots. Our inclusion of methods that have not been used before in this context broadens the set of available detection methods and compares them against the current state-of-the-art methods for subcellular particle detection.</p

ZebIAT, an image analysis tool for registering zebrafish embryos and quantifying cancer metastasis

BACKGROUND: Zebrafish embryos have recently been established as a xenotransplantation model of the metastatic behaviour of primary human tumours. Current tools for automated data extraction from the microscope images are restrictive concerning the developmental stage of the embryos, usually require laborious manual image preprocessing, and, in general, cannot characterize the metastasis as a function of the internal organs. METHODS: We present a tool, ZebIAT, that allows both automatic or semi-automatic registration of the outer contour and inner organs of zebrafish embryos. ZebIAT provides a registration at different stages of development and an automatic analysis of cancer metastasis per organ, thus allowing to study cancer progression. The semi-automation relies on a graphical user interface. RESULTS: We quantified the performance of the registration method, and found it to be accurate, except in some of the smallest organs. Our results show that the accuracy of registering small organs can be improved by introducing few manual corrections. We also demonstrate the applicability of the tool to studies of cancer progression. CONCLUSIONS: ZebIAT offers major improvement relative to previous tools by allowing for an analysis on a per-organ or region basis. It should be of use in high-throughput studies of cancer metastasis in zebrafish embryos.Work supported by the Academy of Finland (ASR), Emil Aaltonen Foundation (EL), and the Finnish Funding Agency for Technology and Innovation (ASR,TA). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.S

Cholesterol impairment contributes to neuroserpin aggregation

Intraneural accumulation of misfolded proteins is a common feature of several neurodegenerative pathologies including Alzheimer's and Parkinson's diseases, and Familial Encephalopathy with Neuroserpin Inclusion Bodies (FENIB). FENIB is a rare disease due to a point mutation in neuroserpin which accelerates protein aggregation in the endoplasmic reticulum (ER). Here we show that cholesterol depletion induced either by prolonged exposure to statins or by inhibiting the sterol regulatory binding-element protein (SREBP) pathway also enhances aggregation of neuroserpin proteins. These findings can be explained considering a computational model of protein aggregation under non-equilibrium conditions, where a decrease in the rate of protein clearance improves aggregation. Decreasing cholesterol in cell membranes affects their biophysical properties, including their ability to form the vesicles needed for protein clearance, as we illustrate by a simple mathematical model. Taken together, these results suggest that cholesterol reduction induces neuroserpin aggregation, even in absence of specific neuroserpin mutations. The new mechanism we uncover could be relevant also for other neurodegenerative diseases associated with protein aggregation.Comment: 7 figure

AN AUTOMATIC SYSTEM FOR THE ANALYSIS OF INTERCELLULAR COMMUNICATION AND EARLY CARCINOGENESIS

International audienceSome recent works on intercellular communication pointed out an impaired trafficking of Cx43 proteins in early carcinogenesis. In collaboration with biologists, we propose an automatic system for the analysis of spatial protein configurations within cells at early tumor stages. This system is an essential step towards the future development of a computer-aided diagnosis tool and the statistical validation of biological hypotheses about Cx43 expressions and configurations during tumorogenesis. The proposed system contains two dependent part: a segmentation part in which the cell structures of interest are automatically located on images and a characterization part in which some spatial features are computed for the classification of cells. Using immunofluorescent images of cells, the nucleus, cytoplasm and proteins structures within the cell are extracted. Then, some spatial features are computed to characterize spatial configurations of the proteins with regard to the nucleus and cytoplasm areas in the image. Last, the 3D cell images are classified into pathogenic or viable classes. The system has been quantitatively evaluated over 60 cell images acquired by a deconvolution high-resolution microscope and whose ground truth has been manually given by a biologist expert. As a perspective, a 3D spatial reasoning and visualization module is currently under development

A 3D-printed microfluidic-enabled hollow microneedle architecture for transdermal drug delivery.

Embedding microfluidic architectures with microneedles enables fluid management capabilities that present new degrees of freedom for transdermal drug delivery. To this end, fabrication schemes that can simultaneously create and integrate complex millimeter/centimeter-long microfluidic structures and micrometer-scale microneedle features are necessary. Accordingly, three-dimensional (3D) printing techniques are suitable candidates because they allow the rapid realization of customizable yet intricate microfluidic and microneedle features. However, previously reported 3D-printing approaches utilized costly instrumentation that lacked the desired versatility to print both features in a single step and the throughput to render components within distinct length-scales. Here, for the first time in literature, we devise a fabrication scheme to create hollow microneedles interfaced with microfluidic structures in a single step. Our method utilizes stereolithography 3D-printing and pushes its boundaries (achieving print resolutions below the full width half maximum laser spot size resolution) to create complex architectures with lower cost and higher print speed and throughput than previously reported methods. To demonstrate a potential application, a microfluidic-enabled microneedle architecture was printed to render hydrodynamic mixing and transdermal drug delivery within a single device. The presented architectures can be adopted in future biomedical devices to facilitate new modes of operations for transdermal drug delivery applications such as combinational therapy for preclinical testing of biologic treatments

Mobility of daughter elements of U-238 decay chain during leaching by In Situ Recovery (ISR) : New insights from digital autoradiography

In highly permeable sedimentary rock formations, U extraction by in-situ leaching techniques (ISR - In-Situ Recovery) is generally considered to have a limited environmental impact at ground level. Significantly, this method of extraction produces neither mill tailings nor waste rocks. Underground, however, the outcome for U-238 daughter elements in aquifers is not well known because of their trace concentrations in the host rocks. Thus, understanding the in-situ mobility of these elements remains a challenge. Two samples collected before and after six months of ISR experiments (Dulaan Uul, Mongolia) were studied with the help of a digital autoradiography technique (DA) of alpha particles, bulk alpha spectrometry, and complementary petrographic observation methods. These techniques demonstrate that before and after leaching, the radioactivity is concentrated in altered and microporous Fe-Ti oxides. Most of the daughter elements of U remain trapped in the rock after the leaching process. DA confirms that the alpha activity of the Fe-Ti oxides remains high after uranium leaching, and the initial secular equilibrium of the U-238 series for Th-230 to Po-210 daughter elements (including Ra-226) of the fresh rocks is maintained after leaching. While these findings should be confirmed by more systematic studies, they already identify potential mechanisms explaining why the U-daughter concentrations in leaching water are low.Peer reviewe