Image Analysis Software Package Research Articles

The role of Galectin-1 in HIV associated preeclampsia

ObjectiveIn this study, the role of Gal1, a regulatory protein involved in receptor binding and gene transcription within trophoblast cells, in the pathophysiology of HIV associated preeclampsia was determined by immunolocalizing its expression in the placenta of a South African cohort. Study Designthis is an analytical study carried out at the Optics and Imaging Center, Neslon R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.A hundred and twenty HIV negative or positive, Black African primigrad or multigravid women with pre-eclamptic and normotensive pregnancies were involved in the study.Post-delivery, full thickness of centrally located placental tissue obtained was fixed for immunohistochemistry. The expression of Gal1 was immunolocalized using immunohistochemical assay kit and further quantified with using AxioVision Image analysis software package. Student t-test was used to compare the levels of the analytes while One-way ANOVA was used for comparison across the groups. ResultsGal1 immunoreactivity was observed within the Hofbauer cells, cytotrophoblast, syncytial knots and in the endothelial cells lining blood vessels in both exchange and conducting villi of both normotensive and preeclamptic pregnancies regardless of HIV status. There was a down regulation in Gal1 immunoreactivity in both the exchange and conducting villi of preeclamptic compared to normotensive pregnancies. However, there was no significant effect of HIV infection on Gal1 immunostaining in both villi types. ConclusionThe down regulation of Gal1 in preeclampsia may be due to the inhibition of the MAPK pathway. Since Gal1 influences differentiation and migration, the defective trophoblast invasion in preeclampsia may emanate from its decreased immunoexpression. This highlights the role of Gal1 in angiogenesis and placentation.

A Study of Contact Interface for an Anti-Rotation Rivet Using Ultrasonic Detection

This work measures the contact area between an anti-rotation rivet and an aluminum plate under different riveting loads based on the regional scanning of ultrasound. The contact image is a novel disclosure for the anti-rotation rivet contact. The 2D maps show an apparent change not only in area sizes but also in contact shapes under various normal forces applied. The 3D contact images also provide useful information to show the intensity of contact. The contact area between the anti-rotation rivet and the aluminum is calculated using an image analysis software package. The range of contact areas varies from 6.3 mm2 to 57.2 mm2, depending on the applied forces and the definition of the contrast ratio. Furthermore, a calibration of data fitting is performed to provide a useful polynomial equation for contact area estimation. In addition, maps of both a reflection coefficient and a pressure contour distribution are presented. The range of peak contact pressure varies from 7.1 MPa to 11.2 MPa.

High-precision angular measurement of 12C ion interaction using a new imaging method with a CR-39 detector in the energy range below 100 MeV/nucleon

In this study, we show that angular measurement of nuclear tracks produced in heavy ion interactions can be made with high precision using a CR-39 solid-state nuclear track detector. For this purpose, we have increased the position resolution of nuclear track (etch pit) analysis and the precission of thickness measurement of the CR-39 detector. The position resolution of the heavy ion track was verified to be 0.02 μm by the dedicated image analysis software package PitFit. The precision of the thickness measurement of the CR-39 detector was increased to 0.6 μm by our new both sides imaging method of the CR-39 detector using the autofocus system of the microscope. As a consequence, the angular distributions of projectiles and fragments can be realized with a precision of 1.4 × 10−2 degrees (2.5 × 10−4 radian). As a demonstration, we applied the angular measurement technique to the diagnosis of heavy ion beam and the small Coulomb scattering angle measurement of interactions of 12C + Al in energies below 100 MeV/nucleon. By this new imaging technique, event-by-event interaction of the projectiles in the CR-39 detector can be measured rapidly and can be applied to the measurement of the total charge-changing cross section, the decay mode, and the branching ratios of the projectile with higher angular precision.

Live Monitoring and Analysis of Fungal Growth, Viability, and Mycelial Morphology Using the IncuCyte NeuroTrack Processing Module.

Efficient live-imaging methods are pivotal to understand fungal morphogenesis, especially as it relates to interactions with host immune cells and mechanisms of antifungal drugs. Due to the notable similarities in growth patterns of neuronal cells and mycelial networks, we sought to repurpose the NeuroTrack (NT) processing module of the IncuCyte time-lapse microscopy system as a tool to quantify mycelial growth and branching of pathogenic fungi. We showed the robustness of NT analysis to study Candida albicans and five different molds and confirmed established characteristics of mycelial growth kinetics. We also documented high intra- and interassay reproducibility of the NT module for a spectrum of spore inocula and culture periods. Using GFP-expressing Aspergillus fumigatus and Rhizopus arrhizus, the feasibility of fluorescence-based NT analysis was validated. In addition, we performed proof-of-concept experiments of NT analysis for several translational applications such as studying the morphogenesis of a filamentation-defective C. albicans mutant, the effects of different classes of antifungals (polyenes, azoles, and echinocandins), and coculture with host immune cells. High accuracy was found, even at high immune cell-to-fungus ratios or in the presence of fungal debris. For antifungal efficacy studies, addition of a cytotoxicity dye further refined IncuCyte-based analysis, facilitating real-time determination of fungistatic and fungicidal activity in a single assay. Complementing conventional MIC-based assays, NT analysis is an appealing method to study fungal morphogenesis and viability in the context of antifungal compound screening and evaluation of novel immune therapeutics.IMPORTANCE Pathogenic fungi remain a major cause of infectious complications in immunocompromised patients. Microscopic techniques are crucial for our understanding of fungal biology, host-pathogen interaction, and the pleiotropic effects of antifungal drugs on fungal cell growth and morphogenesis. Taking advantage of the morphological similarities of neuronal cell networks and mycelial growth patterns, we employed the IncuCyte time-lapse microscopy system and its NeuroTrack image analysis software package to study growth and branching of a variety of pathogenic yeasts and molds. Using optimized image processing definitions, we validated IncuCyte NeuroTrack analysis as a reliable and efficient tool for translational applications such as antifungal efficacy evaluation and coculture with host immune effector cells. Hence, the IncuCyte system and its NeuroTrack module provide an appealing platform for efficient in vitro studies of antifungal compounds and immunotherapeutic strategies in medical mycology.

Comparison of accuracy of the maxillary sinus area and dimensions for sex estimation lateral cephalograms of Iranian samples

Abstract Background Sex estimation is a critical issue in forensic medicine. Since anthropologic evaluations on radiographs can contribute to more accurate sex estimation, this study measured the length and height, as well as area, of the maxillary sinus on lateral cephalometric radiography. Methods and materials In this descriptive-analytic study, 80 images obtained from 20 to 40-year-old individuals (40 males and 40 female) were selected. The height and anterior-posterior length of the maxillary sinus was performed using CATIA V5R20 (a software package for image analysis). Maxillary sinus area was determined using discriminant analysis in AutoCAD. Findings The mean maxillary sinus height was 40.48 mm in males and 38.7 mm in females. The mean maxillary sinus length was 40.31 mm in males and 37.31 mm in females. The area of the maxillary sinus was 1201.2 mm2 in males and 1043.4 mm2 in females. Two discriminant analysis models, one based on the height and length of the maxillary sinus and the other based on sinus area) were developed for sex estimation. The area under the receiver operating characteristic (ROC) curve was used for quality assessment of the fitted models and determination of their prediction ability. Conclusion The mean height, length and area of the maxillary sinus were significantly larger in males than in females (P

МОРФОМЕТРИЧЕСКАЯ ХАРАКТЕРИСТИКА ТЕРМИНАЛЬНЫХ ВОРСИН ПЛАЦЕНТЫ ПРИ НЕДОНОШЕННОСТИ

In this study, morphometric features of terminal villi in term and preterm placentas were compared. Placentas of 13 patients whose pregnancy ended in premature birth and placentas of 35 women with physiological pregnancy and delivery at term were studied. Morphometric assessment was made with Carl Zeiss Axio Imager microscope using an image analysis software package. The number of capillaries in terminal villi of preterm placentas was found to be decreased, while the vessels-to-syncytiotrophoblast distance was found to be increased. These result in a decreased gas exchange between maternal blood and placental tissue, hypoxia and can cause early termination of pregnancy. Mean values of cross-sectional area, vertical dimension and perimeter of terminal villi in preterm placentas are found to be greater than those in term placentas, which contributed to an increase in gas exchange area and can be regarded as a compensatory reaction at a tissue level.

Moving into a new dimension: Tracking migrating cells with digital holographic cytometry in 3D.

Moving into a new dimension : Tracking migrating cells with digital holographic cytometry in 3D

Evaluation of holographic imaging cytometer holomonitor M4® motility applications.

Digital holographic cytometry (DHC) and other methods of quantitative phase imaging permit extended time-lapse imaging of mammalian cells in the absence of induced cellular toxicity. Manufactured DHC platforms equipped with semi-automated image acquisition, segmentation, and analysis software packages (or modules) for assessing cell behavior are now commercially available. When housed in mammalian cell incubators these cytometers offer the potential to monitor and quantify a range of cellular behaviors without disrupting routine culture. Realization of this potential requires validation against established standards. Two proprietary software modules for assessing cellular motility available using the HoloMonitor M4 DHC platform were evaluated on human melanoma cells lines with known relative motility and metastatic potential. One such software package, the Track Cells module, was run during routine culture. In addition, the Wound Healing module was conducted in parallel with established transwell migration and invasion assays. Each module was evaluated for reproducibility and correlation to established assays. Both software modules reliably recorded increased cellular motility in the metastatic 1205Lu line as compared with the non-metastatic WM793 line. In a direct comparison of the two propriety DHC software modules and two established transwell assays, the relative cell motilities were well correlated. The granularity of data provided by the Track Cells module permitted the additional identification of rare hyper-motile cells in the metastatic population and the distinction of motility from division associated displacement. The two HoloMonitor M4 DHC proprietary software modules for assessing cellular motility yielded reproducible results that were well-correlated with established standards. © 2018 International Society for Advancement of Cytometry.

New surface characterization tools for alumina based refractory material exposed to cavitation - Image analysis and pattern recognition approach

The aim of this study was to examine the influence of cavitation erosion on the morphology of defects formed on the surfaces of alumina-based materials. The alumina-based samples were exposed to cavitation erosion for 42 min. The damages that occurred were monitored at predefined time intervals by measuring the mass loss and observing the sample surfaces. Digital images of surfaces were processed using an image analysis software package to define morphological characteristics of the damages occurred. The calculated morphological parameters were subjected to analysis by pattern recognition techniques to correlate the appearance of particular morphological characteristics with the behavior of the material during cavitation erosion. The newly established method in describing cavitation erosion which uses pattern recognition approach for treatments of morphological parameters calculated for damages by image analysis tools gave the results efficient for material characterization as the traditional one.

Quantifying Branching Density in Rat Mammary Gland Whole-mounts Using the Sholl Analysis Method

An increasing number of studies are utilizing the rodent mammary gland as an endpoint for assessing the developmental toxicity of a chemical exposure. The effects these exposures have on mammary gland development are typically evaluated using either basic dimensional measurements or by scoring morphological characteristics. However, the broad range of methods for interpreting developmental changes could lead to inconsistent translations across laboratories. A common method of assessment is needed so that proper interpretations can be formed from data being compared across studies. The present study describes the application of the Sholl analysis method to quantify mammary gland branching characteristics. The Sholl method was originally developed for use in quantifying neuronal dendritic patterns. By using ImageJ, an open-source image analysis software package, and a plugin developed for this analysis, the mammary gland branching density and the complexity of a mammary gland from a peripubertal female rat were determined. The methods described here will enable the use of the Sholl analysis as an effective tool for quantifying an important characteristic of mammary gland development.

Quantifying Branching Density in Rat Mammary Gland Whole-mounts Using the Sholl Analysis Method.

An increasing number of studies are utilizing the rodent mammary gland as an endpoint for assessing the developmental toxicity of a chemical exposure. The effects these exposures have on mammary gland development are typically evaluated using either basic dimensional measurements or by scoring morphological characteristics. However, the broad range of methods for interpreting developmental changes could lead to inconsistent translations across laboratories. A common method of assessment is needed so that proper interpretations can be formed from data being compared across studies. The present study describes the application of the Sholl analysis method to quantify mammary gland branching characteristics. The Sholl method was originally developed for use in quantifying neuronal dendritic patterns. By using ImageJ, an open-source image analysis software package, and a plugin developed for this analysis, the mammary gland branching density and the complexity of a mammary gland from a peripubertal female rat were determined. The methods described here will enable the use of the Sholl analysis as an effective tool for quantifying an important characteristic of mammary gland development.

Automated “Bone Subtraction” Image Analysis Software Package for Improved and Faster CT Monitoring of Longitudinal Spine Involvement in Patients with Multiple Myeloma

The study aimed to assess the diagnostic benefit of a novel computed tomography (CT) post-processing software generating subtraction maps of longitudinal non-enhanced CT examinations for monitoring the course of myeloma bone disease in the spine. The local institutional review board approved the retrospective data evaluation. Included were 82 consecutive myeloma patients (46 male; mean age, 65.08 ± 9.76) who underwent 188 repeated whole-body reduced-dose Multislice Detector Computed Tomography (MDCT) at our institution between December 2013 and January 2016. Lytic bone lesions were categorized as new or enlarging versus stable. Bone subtraction maps were read in combination with corresponding 1-mm source images comparing results to those of standard image reading of 5-mm axial and 2-mm multiplanar reformat reconstructions (MPR) scans and hematologic markers, and classified as either progressive disease (PD) or stable disease (SD or remission). The standard of reference was 1-mm axial CT image reading + hematologic response both confirmed at follow-up. For statistical purposes, we subgrouped the hematologic response categories similarly to those applied for CT imaging (progression vs stable/response). According to the standard of reference, 16 patients experienced PD and 66 SD at follow-up. Th sensitivity, specificity, and accuracy for axial 5 mm + 2 mm MPR image versus bone subtraction maps in a "lesion-by-lesion" reading were 97.6%, 92.3%, and 97.2% versus 97.8%, 96.7%, and 97.7%, respectively. The use of bone subtraction maps resulted in a change of response classification in 9.7% of the patients (n = 8) versus 5 mm + 2 mm MPR image reading from SD to PD. Bone sclerosis lesions were detected in 52 out of 82 patients (63.4%). The reading time was significantly lower with the software bone subtraction compared to standard reading (P < 0.01) and 1-mm image reading (P < 0.001). Accuracy of bone subtraction maps reading for monitoring multiple myeloma is slightly increased over that of conventional axial + MPR image reading and significantly speeds up the reading time.

MiToBo - A Toolbox for Image Processing and Analysis

MiToBo is a toolbox and Java library for solving basic as well as advanced image processing and analysis tasks. It features a rich collection of fundamental, intermediate and high-level image processing operators and algorithms as well as a couple of sophisticated tools for specific biological and biomedical applications. These tools include operators for elucidating cellular morphology and locomotion as well as operators for the characterization of certain intracellular particles and structures.MiToBo builds upon and integrates into the widely-used image analysis software packages ImageJ and Fiji [11, 10], and all of its operators can easily be run in ImageJ and Fiji via a generic operator runner plugin. Alternatively MiToBo operators can directly be run from command line, and using its functionality as a library for developing own applications is also supported. Thanks to the Alida library [8] forming the base of MiToBo all operators share unified APIs fostering reusability, and graphical as well as command line user interfaces for operators are automatically generated. MiToBo is available from its website http://www.informatik.uni-halle.de/mitobo, on Github, via an Apache Archiva Maven repository server, and it can easily be activated in Fiji via its own update site.

TiLIA: a software package for image analysis of firefly flashpatterns.

As flash signaling patterns of fireflies are species specific, signal‐pattern analysis is important for understanding this system of communication. Here, we present time‐lapse image analysis (TiLIA), a free open‐source software package for signal and flight pattern analyses of fireflies that uses video‐recorded image data. TiLIA enables flight path tracing of individual fireflies and provides frame‐by‐frame coordinates and light intensity data. As an example of TiLIA capabilities, we demonstrate flash pattern analysis of the fireflies Luciola cruciata and L. lateralis during courtship behavior.

High-Content Analysis of CRISPR-Cas9 Gene-Edited Human Embryonic Stem Cells.

SummaryCRISPR-Cas9 gene editing of human cells and tissues holds much promise to advance medicine and biology, but standard editing methods require weeks to months of reagent preparation and selection where much or all of the initial edited samples are destroyed during analysis. ArrayEdit, a simple approach utilizing surface-modified multiwell plates containing one-pot transcribed single-guide RNAs, separates thousands of edited cell populations for automated, live, high-content imaging and analysis. The approach lowers the time and cost of gene editing and produces edited human embryonic stem cells at high efficiencies. Edited genes can be expressed in both pluripotent stem cells and differentiated cells. This preclinical platform adds important capabilities to observe editing and selection in situ within complex structures generated by human cells, ultimately enabling optical and other molecular perturbations in the editing workflow that could refine the specificity and versatility of gene editing.

Iron ore textural information is the key for prediction of downstream process performance

Textural information or information about the presence of porosity, different material or mineral types and their structural arrangement in iron ore is crucial for understanding, predicting and optimising downstream processing performance. Ores with the same chemical and mineral composition may behave very differently during downstream processing due to differences in textural components.To produce a textural description of iron ore, it is preferable to use an automated system to avoid subjectivity and to collect additional information about mineral abundance, liberation and association. CSIRO created a unique dedicated optical image analysis software package for automated textural classification and characterisation of different minerals, sinters and coke. This software, called Mineral4/Recognition4, has been used extensively to collect data for this article.Four case studies of CSIRO research are presented to demonstrate the importance of textural information.•The first example shows that iron ore samples with different texture but similar mineralogy undergo different degrees of assimilation in compact sintering.•The second example shows that empirical modelling of sinter properties was improved considerably after introducing textural information.•The third example demonstrates the application of classification by ore texture to model and optimise hydrocyclone performance.•The last example is an experimental study of ultrasonic treatment of hematitic–goethitic iron ore fines. It demonstrates how the resulting breakdown or deagglomeration of different particles, and the mineral deportment, can be better understood when textural information is also considered.In all cases, the availability of textural information was critical, providing a better prediction of process performance or a deeper understanding of the unit process.

Osteolytica: An automated image analysis software package that rapidly measures cancer-induced osteolytic lesions in in vivo models with greater reproducibility compared to other commonly used methods

Methods currently used to analyse osteolytic lesions caused by malignancies such as multiple myeloma and metastatic breast cancer vary from basic 2-D X-ray analysis to 2-D images of micro-CT datasets analysed with non-specialised image software such as ImageJ. However, these methods have significant limitations. They do not capture 3-D data, they are time-consuming and they often suffer from inter-user variability. We therefore sought to develop a rapid and reproducible method to analyse 3-D osteolytic lesions in mice with cancer-induced bone disease. To this end, we have developed Osteolytica, an image analysis software method featuring an easy to use, step-by-step interface to measure lytic bone lesions. Osteolytica utilises novel graphics card acceleration (parallel computing) and 3-D rendering to provide rapid reconstruction and analysis of osteolytic lesions. To evaluate the use of Osteolytica we analysed tibial micro-CT datasets from murine models of cancer-induced bone disease and compared the results to those obtained using a standard ImageJ analysis method. Firstly, to assess inter-user variability we deployed four independent researchers to analyse tibial datasets from the U266-NSG murine model of myeloma. Using ImageJ, inter-user variability between the bones was substantial (±19.6%), in contrast to using Osteolytica, which demonstrated minimal variability (±0.5%). Secondly, tibial datasets from U266-bearing NSG mice or BALB/c mice injected with the metastatic breast cancer cell line 4T1 were compared to tibial datasets from aged and sex-matched non-tumour control mice. Analyses by both Osteolytica and ImageJ showed significant increases in bone lesion area in tumour-bearing mice compared to control mice. These results confirm that Osteolytica performs as well as the current 2-D ImageJ osteolytic lesion analysis method. However, Osteolytica is advantageous in that it analyses over the entirety of the bone volume (as opposed to selected 2-D images), it is a more rapid method and it has less user variability.

Reference criteria for the timing of the replacement of a six-fluted end-mill cutter

This study investigates the contact interface for both a retired six-fluted end-mill cutter and a new one and then compares them using ultrasonic scanning, surface roughness measurement, and SEM evaluation. This is a static measurement, because the objective is to provide information for wear diagnosis. The relationship between the surface roughness and the contact area of the cutting teeth is also determined. The results show that the retired cutting teeth have an obviously smoother surface roughness and a greater contact area than those of the new cutter. The contact area between the six-fluted end-mill cutter and the specimen is calculated using an image analysis software package. The range of contact areas varies from 7.21 to 49.44 mm2 for the retired cutter and from 2.82 to 37.2 mm2 for the new item, depending on both the contact force and the definition of the contrast ratio. The SEM views of the surface topography of the end-mills under ×200, ×400, and ×800 magnifications are also presented.

2D-gel spot detection and segmentation based on modified image-aware grow-cut and regional intensity information

BackgroundProteomics, the study of proteomes, has been increasingly utilized in a wide variety of biological problems. The Two-Dimensional Gel Electrophoresis (2D-PAGE) technique is a powerful proteomics technique aiming at separation of the complex protein mixtures. Spot detection and segmentation are fundamental components of 2D-gel image analysis but remain arduous and difficult tasks. Several software packages and academic approaches are available for 2D-gel image spot detection and segmentation. Each one has its respective advantages and disadvantages and achieves a different level of success in dealing with the challenges of 2D-gel image analysis. A common characteristic of the available methods is their dependency on user intervention in order to achieve optimal results, a process that can lead to subjective and non-reproducible results. In this work, the authors propose a novel spot detection and segmentation methodology for 2D-gel images. MethodsThis work introduces a novel spot detection and spot segmentation methodology that is based on a multi-thresholding scheme applied on overlapping regions of the image, a custom grow-cut algorithm, a region growing scheme and morphological operators. The performance of the proposed methodology is evaluated on real as well as synthetic 2D-gel images using well established statistical measures, including precision, sensitivity, and their weighted measure, F-measure, as well as volumetric overlap, volumetric error and volumetric overlap error. ResultsExperimental results show that the proposed methodology outperforms state-of-the-art software packages and methods proposed in the literature and results in more plausible spot boundaries and more accurate segmentation. The proposed method achieved the highest F-measure (94.8%) for spot detection and the lowest volumetric overlap error (8.3%) for the segmentation process. ConclusionsEvaluation against state-of-the-art 2D-gel image analysis software packages and techniques proposed in the literature, including Melanie 7, Delta2D, PDQuest and Scimo, demonstrates that the proposed approach outperforms the other methods evaluated in this work and constitutes an advantageous and reliable solution for 2D-gel image analysis.

Head motion during MRI acquisition reduces gray matter volume and thickness estimates

Imaging biomarkers derived from magnetic resonance imaging (MRI) data are used to quantify normal development, disease, and the effects of disease-modifying therapies. However, motion during image acquisition introduces image artifacts that, in turn, affect derived markers. A systematic effect can be problematic since factors of interest like age, disease, and treatment are often correlated with both a structural change and the amount of head motion in the scanner, confounding the ability to distinguish biology from artifact. Here we evaluate the effect of head motion during image acquisition on morphometric estimates of structures in the human brain using several popular image analysis software packages (FreeSurfer 5.3, VBM8 SPM, and FSL Siena 5.0.7). Within-session repeated T1-weighted MRIs were collected on 12 healthy volunteers while performing different motion tasks, including two still scans. We show that volume and thickness estimates of the cortical gray matter are biased by head motion with an average apparent volume loss of roughly 0.7%/mm/min of subject motion. Effects vary across regions and remain significant after excluding scans that fail a rigorous quality check. In view of these results, the interpretation of reported morphometric effects of movement disorders or other conditions with increased motion tendency may need to be revisited: effects may be overestimated when not controlling for head motion. Furthermore, drug studies with hypnotic, sedative, tranquilizing, or neuromuscular-blocking substances may contain spurious “effects” of reduced atrophy or brain growth simply because they affect motion distinct from true effects of the disease or therapeutic process.