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In this paper, we propose a combination of mean-shift-based tracking processes to establish migrating cell trajectories through in vitro phase-contrast video microscopy. After a recapitulation on how the mean-shift algorithm permits efficient object tracking we describe the proposed extension and apply it to the in vitro cell tracking problem. In this application, the cells are unmarked (i.e., no fluorescent probe is used) and are observed under classical phase-contrast microscopy. By introducing an adaptive combination of several kernels, we address several problems such as variations in size and shape of the tracked objects (e.g., those occurring in the case of cell membrane extensions), the presence of incomplete (or noncontrasted) object boundaries, partially overlapping objects and object splitting (in the case of cell divisions or mitoses). Comparing the tracking results automatically obtained to those generated manually by a human expert, we tested the stability of the different algorithm parameters and their effects on the tracking results. We also show how the method is resistant to a decrease in image resolution and accidental defocusing (which may occur during long experiments, e.g., dozens of hours). Finally, we applied our methodology on cancer cell tracking and showed that cytochalasin-D significantly inhibits cell motility. Index Terms--Cell division, cell motility, image processing, mean-shift, tracking, video microscopy.

The aim of this study was to describe and analyze the regulation and spatio-temporal dynamics of melanocyte migration in vitro and its coupling to cell division and interaction with the matrix. The melanocyte lineage is particularly interesting because it is involved in both embryonic development and oncogenesis/metastasis (melanoma). Biological experiments were performed on two melanocyte cell lines established from wild-type and β-catenin-transgenic mice (bcat*). The multi-functional β-catenin molecule is known to be able to regulate the transcription of various genes involved in cell proliferation and migration, particularly in the melanocyte lineage. We also investigated fibronectin, an extra-cellular matrix protein that binds integrins, thereby providing adhesion points for cells and encouraging migration. As the migration of individual cells were followed, automated methods were required for processing the large amount of data generated by the time-lapse video-microscopy. A model-based approach for automated cell tracking was evaluated on a sample by comparison with manual tracking. This method was found reliable in studying overall cell behaviour. Its application to all the observed sequences provided insight into the factors affecting melanocyte migration in vitro: melanocytes of mutated form of β-catenin showed higher division rates and no contact inhibition of growth was induced by the resulting increase in cell density. However, cell density limited the amplitude of cell displacements, although their motility was less affected. The high fibronectin concentration bound to substratum promoted cell migration and motility, the effect being more intense for wild-type cells than for cells with β-catenin over-expression. During the division process, cell migration speed increased rapidly then decreased slowly. Analyses of such data is expected to lead both to biological answers and to a framework for a better modeling processes in the future. [ABSTRACT FROM PUBLISHER]

When an artist conceives a masterpiece, by working on a scaled model, their primary objective is to match the idea of what the art work should be, not to make a digital version that fulfills the engineering requirements. Olivier Strebelle's "Athletes' Alley" will be, in its final version, approximately 30 m tall and more than 100 m long and will be built in Beijing for the next Olympic games. We describe in this paper how we tackled the digitizing of the scaled model made by the artist in order to give the most precise digital model possible compatible with the engineering software. The original artist's model is made of stainless steel arcs welded together into a complex 3D wired light weight sculpture. The main challenges of this development were that no existing 3D scanner was adapted for this acquisition and that the time constraint to do the task was very short. Due to the model's complexity, we opted for a point-by-point acquisition with a high resolution surgical localizer, combined with an automatic filtering algorithm based on a priori knowledge of the sculpture. In summary we manage to perform the 3D geometry acquisition of a very complex structure by diverting the use of a medical 3D localizer where the commonly used 3D digitizers could not do the job. [ABSTRACT FROM AUTHOR]

Panoptic Quality (PQ), designed for the task of "Panoptic Segmentation" (PS), has been used in several digital pathology challenges and publications on cell nucleus instance segmentation and classification (ISC) since its introduction in 2019. Its purpose is to encompass the detection and the segmentation aspects of the task in a single measure, so that algorithms can be ranked according to their overall performance. A careful analysis of the properties of the metric, its application to ISC and the characteristics of nucleus ISC datasets, shows that is not suitable for this purpose and should be avoided. Through a theoretical analysis we demonstrate that PS and ISC, despite their similarities, have some fundamental differences that make PQ unsuitable. We also show that the use of the Intersection over Union as a matching rule and as a segmentation quality measure within PQ is not adapted for such small objects as nuclei. We illustrate these findings with examples taken from the NuCLS and MoNuSAC datasets. The code for replicating our results is available on GitHub ( https://github.com/adfoucart/panoptic-quality-suppl )., (© 2023. The Author(s).)

Desertification is one of the most destructive climate-related issues in the Sudan-Sahel region of Africa. As the assessment of desertification is possible by satellite image analysis using vegetation indices (VIs), this study reports on the technical advantages and capabilities of scripting the 'raster' and 'terra' R-language packages for computing the VIs. The test area which was considered includes the region of the confluence between the Blue and White Niles in Khartoum, southern Sudan, northeast Africa and the Landsat 8-9 OLI/TIRS images taken for the years 2013, 2018 and 2022, which were chosen as test datasets. The VIs used here are robust indicators of plant greenness, and combined with vegetation coverage, are essential parameters for environmental analytics. Five VIs were calculated to compare both the status and dynamics of vegetation through the differences between the images collected within the nine-year span. Using scripts for computing and visualising the VIs over Sudan demonstrates previously unreported patterns of vegetation to reveal climate-vegetation relationships. The ability of the R packages 'raster' and 'terra' to process spatial data was enhanced through scripting to automate image analysis and mapping, and choosing Sudan for the case study enables us to present new perspectives for image processing.

Introduction: Over the last 5 years, the analysis of respiratory patterns presents a growing usage in clinical and research purposes, but there is still currently a lack of easy-to-use and affordable devices to perform such kind of evaluation., Objectives: The aim of this study is to validate a new specifically developed method, based on Kinect sensor, to assess respiratory patterns against spirometry under various conditions., Methods: One hundred and one participants took parts in one of the three validations studies. Twenty-five chronic respiratory disease patients (14 with chronic obstructive pulmonary disease (COPD) [65 ± 10 years old, FEV 1  = 37 (15% predicted value), VC = 62 (20% predicted value)], and 11 with lung fibrosis (LF) [64 ± 14 years old, FEV 1  = 55 (19% predicted value), VC = 62 (20% predicted value)]) and 76 healthy controls (HC) were recruited. The correlations between the signal of the Kinect (depth and respiratory rate) and the spirometer (tidal volume and respiratory rate) were computed in part 1. We then included 66 HC to test the ability of the system to detect modifications of respiratory patterns induced by various conditions known to modify respiratory pattern (cognitive load, inspiratory load and combination) in parts 2 and 3., Results: There is a strong correlation between the depth recorded by the Kinect and the tidal volume recorded by the spirometer: r = 0.973 for COPD patients, r = 0.989 for LF patients and r = 0.984 for HC. The Kinect is able to detect changes in breathing patterns induced by different respiratory disturbance conditions, gender and oral task., Conclusions: Measurements performed with the Kinect sensors are highly correlated with the spirometer in HC and patients with COPD and LF. Kinect is also able to assess respiratory patterns under various loads and disturbances. This method is affordable, easy to use, fully automated and could be used in the current clinical context. Respiratory patterns are important to assess in daily clinics. However, there is currently no affordable and easy-to-use tool to evaluate these parameters in clinics. We validated a new system to assess respiratory patterns using the Kinect sensor in patients with chronic respiratory diseases., (© 2023 The Authors. The Clinical Respiratory Journal published by John Wiley & Sons Ltd.)

Digital pathology image analysis challenges have been organised regularly since 2010, often with events hosted at major conferences and results published in high-impact journals. These challenges mobilise a lot of energy from organisers, participants, and expert annotators (especially for image segmentation challenges). This study reviews image segmentation challenges in digital pathology and the top-ranked methods, with a particular focus on how reference annotations are generated and how the methods' predictions are evaluated. We found important shortcomings in the handling of inter-expert disagreement and the relevance of the evaluation process chosen. We also noted key problems with the quality control of various challenge elements that can lead to uncertainties in the published results. Our findings show the importance of greatly increasing transparency in the reporting of challenge results, and the need to make publicly available the evaluation codes, test set annotations and participants' predictions. The aim is to properly ensure the reproducibility and interpretation of the results and to increase the potential for exploitation of the substantial work done in these challenges., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Archived seismograms recorded in the 20th century present a valuable source of information for monitoring earthquake activity. However, old data, which are only available as scanned paper-based images should be digitised and converted from raster to vector format prior to reuse for geophysical modelling. Seismograms have special characteristics and specific featuresrecorded by a seismometer and encrypted in the images: signal trace lines, minute time gaps, timing and wave amplitudes. This information should be recognised and interpreted automatically when processing archives of seismograms containing large collections of data. The objective was to automatically digitise historical seismograms obtained from the archives of the Royal Observatory of Belgium (ROB). The images were originallyrecorded by the Galitzine seismometer in 1954 in Uccle seismic station, Belgium. A dataset included 145 TIFF images which required automatic approach of data processing. Software for digitising seismograms are limited and many have disadvantages. We applied the DigitSeis for machine-based vectorisation and reported here a full workflowof data processing. This included pattern recognition, classification, digitising, corrections and converting TIFFs to the digital vector format. The generated contours of signals were presented as time series and converted into digital format (mat files) which indicated information on ground motion signals contained in analog seismograms. We performed the quality control of the digitised traces in Python to evaluate the discriminating functionality of seismic signals by DigitSeis. We shown a robust approach of DigitSeis as a powerful toolset for processing analog seismic signals. The graphical visualisation of signal traces and analysis of the performed vectorisation results shown that the algorithms of data processing performed accurately and can be recommended in similar applications of seismic signal processing in future related works in geophysical research.

Ballistocardiography (BCG) and seismocardiography (SCG) are non-invasive techniques used to record the micromovements induced by cardiovascular activity at the body's center of mass and on the chest, respectively. Since their inception, their potential for evaluating cardiovascular health has been studied. However, both BCG and SCG are impacted by respiration, leading to a periodic modulation of these signals. As a result, data processing algorithms have been developed to exclude the respiratory signals, or recording protocols have been designed to limit the respiratory bias. Reviewing the present status of the literature reveals an increasing interest in applying these techniques to extract respiratory information, as well as cardiac information. The possibility of simultaneous monitoring of respiratory and cardiovascular signals via BCG or SCG enables the monitoring of vital signs during activities that require considerable mental concentration, in extreme environments, or during sleep, where data acquisition must occur without introducing recording bias due to irritating monitoring equipment. This work aims to provide a theoretical and practical overview of cardiopulmonary interaction based on BCG and SCG signals. It covers the recent improvements in extracting respiratory signals, computing markers of the cardiorespiratory interaction with practical applications, and investigating sleep breathing disorders, as well as a comparison of different sensors used for these applications. According to the results of this review, recent studies have mainly concentrated on a few domains, especially sleep studies and heart rate variability computation. Even in those instances, the study population is not always large or diversified. Furthermore, BCG and SCG are prone to movement artifacts and are relatively subject dependent. However, the growing tendency toward artificial intelligence may help achieve a more accurate and efficient diagnosis. These encouraging results bring hope that, in the near future, such compact, lightweight BCG and SCG devices will offer a good proxy for the gold standard methods for assessing cardiorespiratory function, with the added benefit of being able to perform measurements in real-world situations, outside of the clinic, and thus decrease costs and time.

In this paper, we propose an advanced scripting approach using Python and R for satellite image processing and modelling terrain in Côte d'Ivoire, West Africa. Data include Landsat 9 OLI/TIRS C2 L1 and the SRTM digital elevation model (DEM). The EarthPy library of Python and 'raster' and 'terra' packages of R are used as tools for data processing. The methodology includes computing vegetation indices to derive information on vegetation coverage and terrain modelling. Four vegetation indices were computed and visualised using R: the Normalized Difference Vegetation Index (NDVI), Enhanced Vegetation Index 2 (EVI2), Soil-Adjusted Vegetation Index (SAVI) and Atmospherically Resistant Vegetation Index 2 (ARVI2). The SAVI index is demonstrated to be more suitable and better adjusted to the vegetation analysis, which is beneficial for agricultural monitoring in Côte d'Ivoire. The terrain analysis is performed using Python and includes slope, aspect, hillshade and relief modelling with changed parameters for the sun azimuth and angle. The vegetation pattern in Côte d'Ivoire is heterogeneous, which reflects the complexity of the terrain structure. Therefore, the terrain and vegetation data modelling is aimed at the analysis of the relationship between the regional topography and environmental setting in the study area. The upscaled mapping is performed as regional environmental analysis of the Yamoussoukro surroundings and local topographic modelling of the Kossou Lake. The algorithms of the data processing include image resampling, band composition, statistical analysis and map algebra used for calculation of the vegetation indices in Côte d'Ivoire. This study demonstrates the effective application of the advanced programming algorithms in Python and R for satellite image processing.

Reaction-diffusion models have been proposed for decades to capture the growth of gliomas, the most common primary brain tumors. However, ill-posedness of the initialization at diagnosis time and parameter estimation of such models have restrained their clinical use as a personalized predictive tool. In this work, we investigate the ability of deep convolutional neural networks (DCNNs) to address commonly encountered pitfalls in the field. Based on 1200 synthetic tumors grown over real brain geometries derived from magnetic resonance (MR) data of six healthy subjects, we demonstrate the ability of DCNNs to reconstruct a whole tumor cell-density distribution from only two imaging contours at a single time point. With an additional imaging contour extracted at a prior time point, we also demonstrate the ability of DCNNs to accurately estimate the individual diffusivity and proliferation parameters of the model. From this knowledge, the spatio-temporal evolution of the tumor cell-density distribution at later time points can ultimately be precisely captured using the model. We finally show the applicability of our approach to MR data of a real glioblastoma patient. This approach may open the perspective of a clinical application of reaction-diffusion growth models for tumor prognosis and treatment planning.

Reaction-diffusion models have been proposed for decades to capture the growth of gliomas. Nevertheless, these models require an initial condition: the tumor cell density distribution over the whole brain at diagnosis time. Several works have proposed to relate this distribution to abnormalities visible on magnetic resonance imaging (MRI). In this work, we verify these hypotheses by stereotactic histological analysis of a non-operated brain with glioblastoma using a 3D-printed slicer. Cell density maps are computed from histological slides using a deep learning approach. The density maps are then registered to a postmortem MR image and related to an MR-derived geodesic distance map to the tumor core. The relation between the edema outlines visible on T2-FLAIR MRI and the distance to the core is also investigated. Our results suggest that (i) the previously proposed exponential decrease of the tumor cell density with the distance to the core is reasonable but (ii) the edema outlines would not correspond to a cell density iso-contour and (iii) the suggested tumor cell density at these outlines is likely overestimated. These findings highlight the limitations of conventional MRI to derive glioma cell density maps and the need for other initialization methods for reaction-diffusion models to be used in clinical practice.

Objectives: Multicenter oncology trials increasingly include MRI examinations with apparent diffusion coefficient (ADC) quantification for lesion characterization and follow-up. However, the repeatability and reproducibility (R&R) limits above which a true change in ADC can be considered relevant are poorly defined. This study assessed these limits in a standardized whole-body (WB)-MRI protocol., Methods: A prospective, multicenter study was performed at three centers equipped with the same 3.0-T scanners to test a WB-MRI protocol including diffusion-weighted imaging (DWI). Eight healthy volunteers per center were enrolled to undergo test and retest examinations in the same center and a third examination in another center. ADC variability was assessed in multiple organs by two readers using two-way mixed ANOVA, Bland-Altman plots, coefficient of variation (CoV), and the upper limit of the 95% CI on repeatability (RC) and reproducibility (RDC) coefficients., Results: CoV of ADC was not influenced by other factors (center, reader) than the organ. Based on the upper limit of the 95% CI on RC and RDC (from both readers), a change in ADC in an individual patient must be superior to 12% (cerebrum white matter), 16% (paraspinal muscle), 22% (renal cortex), 26% (central and peripheral zones of the prostate), 29% (renal medulla), 35% (liver), 45% (spleen), 50% (posterior iliac crest), 66% (L5 vertebra), 68% (femur), and 94% (acetabulum) to be significant., Conclusions: This study proposes R&R limits above which ADC changes can be considered as a reliable quantitative endpoint to assess disease or treatment-related changes in the tissue microstructure in the setting of multicenter WB-MRI trials., Key Points: • The present study showed the range of R&R of ADC in WB-MRI that may be achieved in a multicenter framework when a standardized protocol is deployed. • R&R was not influenced by the site of acquisition of DW images. • Clinically significant changes in ADC measured in a multicenter WB-MRI protocol performed with the same type of MRI scanner must be superior to 12% (cerebrum white matter), 16% (paraspinal muscle), 22% (renal cortex), 26% (central zone and peripheral zone of prostate), 29% (renal medulla), 35% (liver), 45% (spleen), 50% (posterior iliac crest), 66% (L5 vertebra), 68% (femur), and 94% (acetabulum) to be detected with a 95% confidence level.

The computer vision community has paid much attention to the development of visible image super-resolution (SR) using deep neural networks (DNNs) and has achieved impressive results. The advancement of non-visible light sensors, such as acoustic imaging sensors, has attracted much attention, as they allow people to visualize the intensity of sound waves beyond the visible spectrum. However, because of the limitations imposed on acquiring acoustic data, new methods for improving the resolution of the acoustic images are necessary. At this time, there is no acoustic imaging dataset designed for the SR problem. This work proposed a novel backprojection model architecture for the acoustic image super-resolution problem, together with Acoustic Map Imaging VUB-ULB Dataset (AMIVU). The dataset provides large simulated and real captured images at different resolutions. The proposed XCycles BackProjection model (XCBP), in contrast to the feedforward model approach, fully uses the iterative correction procedure in each cycle to reconstruct the residual error correction for the encoded features in both low- and high-resolution space. The proposed approach was evaluated on the dataset and showed high outperformance compared to the classical interpolation operators and to the recent feedforward state-of-the-art models. It also contributed to a drastically reduced sub-sampling error produced during the data acquisition.

Recent works have demonstrated the added value of dynamic amino acid positron emission tomography (PET) for glioma grading and genotyping, biopsy targeting, and recurrence diagnosis. However, most of these studies are based on hand-crafted qualitative or semi-quantitative features extracted from the mean time activity curve within predefined volumes. Voxelwise dynamic PET data analysis could instead provide a better insight into intra-tumor heterogeneity of gliomas. In this work, we investigate the ability of principal component analysis (PCA) to extract relevant quantitative features from a large number of motion-corrected [S-methyl- 11 C]methionine ([ 11 C]MET) PET frames. We first demonstrate the robustness of our methodology to noise by means of numerical simulations. We then build a PCA model from dynamic [ 11 C]MET acquisitions of 20 glioma patients. In a distinct cohort of 13 glioma patients, we compare the parametric maps derived from our PCA model to these provided by the classical one-compartment pharmacokinetic model (1TCM). We show that our PCA model outperforms the 1TCM to distinguish characteristic dynamic uptake behaviors within the tumor while being less computationally expensive and not requiring arterial sampling. Such methodology could be valuable to assess the tumor aggressiveness locally with applications for treatment planning and response evaluation. This work further supports the added value of dynamic over static [ 11 C]MET PET in gliomas.

Purpose: To characterize cardiac-driven liver movements using a harmonic phase image representation (HARP) with an optical flow quantification and motion amplification method. The method was applied to define the cardiac trigger delay providing minimal signal losses in liver DWI images., Methods: The 16-s breath-hold balanced-SSFP time resolved 20 images/s were acquired at 3T in coronal and sagittal orientations. A peripheral pulse unit signal was recorded. Cardiac-triggered DWI images were acquired after different peripheral pulse unit delays. A steerable pyramid decomposition with multiple orientations and spatial frequencies was applied. The liver motion field-map was derived from temporal variations of the HARP representation filtered around the cardiac frequency. Liver displacements were quantified with an optical flow method; moreover the right liver motion was amplified., Results: The largest displacements were observed in the left liver (feet-head:3.70 ± 1.06 mm; anterior-posterior: 2.35 ± 0.51 mm). Displacements were statistically significantly weaker in the middle right liver (0.47 ± 0.11 mm; P = 0.0156). The average error was 0.013 ± 0.022 mm (coronal plane) and 0.021 ± 0.041 mm (sagittal plane). The velocity field demonstrated opposing movements of the right liver extremities during the cardiac cycle. DWI signal loss was minimized in regions and instants of smallest amplitude of both velocity and velocity gradient., Conclusion: Cardiac-driven liver movements were quantified with combined cardiac frequency-filtered HARP and optical flow methods. A motion phase opposition between right liver extremities was demonstrated. Displacement amplitude and velocity were larger in the left liver especially along the vertical direction. Motion amplification visually emphasized cardiac-driven right liver displacements. The optimal cardiac timing minimizing signal loss in liver DWI images was derived., (© 2018 International Society for Magnetic Resonance in Medicine.)

In this paper, we propose a method for automatically annotating slide images from colorectal tissue samples. Our objective is to segment glandular epithelium in histological images from tissue slides submitted to different staining techniques, including usual haematoxylin-eosin (H&E) as well as immunohistochemistry (IHC). The proposed method makes use of Deep Learning and is based on a new convolutional network architecture. Our method achieves better performances than the state of the art on the H&E images of the GlaS challenge contest, whereas it uses only the haematoxylin colour channel extracted by colour deconvolution from the RGB images in order to extend its applicability to IHC. The network only needs to be fine-tuned on a small number of additional examples to be accurate on a new IHC dataset. Our approach also includes a new method of data augmentation to achieve good generalisation when working with different experimental conditions and different IHC markers. We show that our methodology enables to automate the compartmentalisation of the IHC biomarker analysis, results concurring highly with manual annotations., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Aim: We evaluated the relationship between IL-8 and prostate cancer (PCa) with emphasis on diagnosis, aggressiveness and prognosis., Materials & Methods: Prostate-specific antigen (PSA) and serum IL-8 were collected from patients undergoing prostate biopsy. IL-8 expression was evaluated on immunohistochemistry with IL-8 labeling index. Complete follow-up of this cohort was achieved over a period of up to 6 years with continuous follow-up of PSA levels., Results: Among 135 patients, serum IL-8 level did not correlate to the diagnosis or aggressiveness of PCa. In 52 radical prostatectomy specimens, a higher IL-8 labeling index was detected in the tumor areas (0.4 ± 0.2 vs 0.33 ± 0.2; p = 0,007) but did not correlate to any of the prognostic markers: D'Amico classification (p = 0.52), Gleason score (p = 0.45), perineural (p = 0.83) and capsular invasion (p = 0.75). No correlation was found to PSA biochemical-free failure., Conclusion: IL-8 serum level was not a significant predictor of diagnosis, aggressiveness or prognosis of PCa., Competing Interests: Financial & competing interests disclosure The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties. No writing assistance was utilized in the production of this manuscript.

Immunohistochemistry (IHC) is a widely used technique in pathology to evidence protein expression in tissue samples. However, this staining technique is known for presenting inter-batch variations. Whole slide imaging in digital pathology offers a possibility to overcome this problem by means of image normalisation techniques. In the present paper we propose a methodology to objectively evaluate the need of image normalisation and to identify the best way to perform it. This methodology uses tissue microarray (TMA) materials and statistical analyses to evidence the possible variations occurring at colour and intensity levels as well as to evaluate the efficiency of image normalisation methods in correcting them. We applied our methodology to test different methods of image normalisation based on blind colour deconvolution that we adapted for IHC staining. These tests were carried out for different IHC experiments on different tissue types and targeting different proteins with different subcellular localisations. Our methodology enabled us to establish and to validate inter-batch normalization transforms which correct the non-relevant IHC staining variations. The normalised image series were then processed to extract coherent quantitative features characterising the IHC staining patterns.

In this paper we address the problem of recovering spatio-temporal trajectories of cancer cells in phase contrast video-microscopy where the user provides the paths on which the cells are moving. The paths are purely spatial, without temporal information. To recover the temporal information associated to a given path we propose an approach based on automatic cell detection and on a graph-based shortest path search. The nodes in the graph consist of the projections of the cell detections onto the geometrical cell path. The edges relate nodes which correspond to different frames of the sequence and potentially to the same cell and trajectory. In this directed graph we search for the shortest path and use it to define a temporal parametrization of the corresponding geometrical cell path. An evaluation based on 286 paths of 7 phase contrast microscopy videos shows that our algorithm allows to recover 92% of trajectory points with respect to the associated ground truth. We compare our method with a state-of-the-art algorithm for semi-automated cell tracking in phase contrast microscopy which requires interactively placed starting points for the cells to track. The comparison shows that supporting geometrical paths in combination with our algorithm allow us to obtain more reliable cell trajectories., (Copyright © 2015 Elsevier B.V. All rights reserved.)

Cell migration research has recently become both a high content and a high throughput field thanks to technological, computational, and methodological advances. Simultaneously, however, urgent bioinformatics needs regarding data management, standardization, and dissemination have emerged. To address these concerns, we propose to establish an open data ecosystem for cell migration research., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

By simultaneously processing a large number of tissue samples, the tissue microarray (TMA) technology allows standardized screening of protein expression using immunohistochemistry thereby providing a very efficient way for tissue-based biomarker analysis. Nowadays, whole slide imaging is becoming standard in digital pathology and enables image sharing, archiving and also processing. In this paper, we present methods for processing TMA images in order to correctly identify the numerous tissue samples and to register images from consecutive TMA sections.

Whole slide scanners are novel devices that enable high-resolution imaging of an entire histological slide. Furthermore, the imaging is achieved in only a few minutes, which enables image rendering of large-scale studies involving multiple immunohistochemistry biomarkers. Although whole slide imaging has improved considerably, locally poor focusing causes blurred regions of the image. These artifacts may strongly affect the quality of subsequent analyses, making a slide review process mandatory. This tedious and time-consuming task requires the scanner operator to carefully assess the virtual slide and to manually select new focus points. We propose a statistical learning method that provides early image quality feedback and automatically identifies regions of the image that require additional focus points.

Cell migration is a key biological process with a role in both physiological and pathological conditions. Locomotion of cells during embryonic development is essential for their correct positioning in the organism; immune cells have to migrate and circulate in response to injury. Failure of cells to migrate or an inappropriate acquisition of migratory capacities can result in severe defects such as altered pigmentation, skull and limb abnormalities during development, and defective wound repair, immunosuppression or tumor dissemination. The ability to accurately analyze and quantify cell migration is important for our understanding of development, homeostasis and disease. In vitro cell tracking experiments, using primary or established cell cultures, are often used to study migration as cells can quickly and easily be genetically or chemically manipulated. Images of the cells are acquired at regular time intervals over several hours using microscopes equipped with CCD camera. The locations (x,y,t) of each cell on the recorded sequence of frames then need to be tracked. Manual computer-assisted tracking is the traditional method for analyzing the migratory behavior of cells. However, this processing is extremely tedious and time-consuming. Most existing tracking algorithms require experience in programming languages that are unfamiliar to most biologists. We therefore developed an automated cell tracking program, written in Java, which uses a mean-shift algorithm and ImageJ as a library. iTrack4U is a user-friendly software. Compared to manual tracking, it saves considerable amount of time to generate and analyze the variables characterizing cell migration, since they are automatically computed with iTrack4U. Another major interest of iTrack4U is the standardization and the lack of inter-experimenter differences. Finally, iTrack4U is adapted for phase contrast and fluorescent cells.

Whole-slide scanners allow the digitization of an entire histological slide at very high resolution. This new acquisition technique opens a wide range of possibilities for addressing challenging image analysis problems, including the identification of tissue-based biomarkers. In this study, we use whole-slide scanner technology for imaging the proliferating activity patterns in tumor slides based on Ki67 immunohistochemistry. Faced with large images, pathologists require tools that can help them identify tumor regions that exhibit high proliferating activity, called "hot-spots" (HSs). Pathologists need tools that can quantitatively characterize these HS patterns. To respond to this clinical need, the present study investigates various clustering methods with the aim of identifying Ki67 HSs in whole tumor slide images. This task requires a method capable of identifying an unknown number of clusters, which may be highly variable in terms of shape, size, and density. We developed a hybrid clustering method, referred to as Seedlink. Compared to manual HS selections by three pathologists, we show that Seedlink provides an efficient way of detecting Ki67 HSs and improves the agreement among pathologists when identifying HSs., (Copyright © 2012 International Society for Advancement of Cytometry.)