Search

Elucidating the dynamics of DNA repair proteins is essential to understanding the mechanisms that preserve genomic stability and prevent carcinogenesis. However, the measurement and modeling of protein dynamics at DNA lesions via currently available image analysis tools is cumbersome. Therefore, we developed CellTool—a stand-alone open-source software with a graphical user interface for the analysis of time-lapse microscopy images. It combines data management, image processing, mathematical modeling, and graphical presentation of data in a single package. Multiple image filters, segmentation, and particle tracking algorithms, combined with direct visualization of the obtained results, make CellTool an ideal application for the comprehensive analysis of DNA repair protein dynamics. This software enables the fitting of obtained kinetic data to predefined or custom mathematical models. Importantly, CellTool provides a platform for easy implementation of custom image analysis packages written in a variety of programing languages. Using CellTool, we demonstrate that the ALKB homolog 2 (ALKBH2) demethylase is excluded from DNA damage sites despite recruitment of its putative interaction partner proliferating cell nuclear antigen (PCNA). Further, CellTool facilitates the straightforward fluorescence recovery after photobleaching (FRAP) analysis of BRCA1 associated RING domain 1 (BARD1) exchange at complex DNA lesions. In summary, the software presented herein enables the time-efficient analysis of a wide range of time-lapse microscopy experiments through a user-friendly interface. [ABSTRACT FROM AUTHOR]

A novel method of extracting color information on a pixel-by-pixel basis or by the average of the regions of interest (ROIs) from digital images is proposed and demonstrated using newly developed and customized image-processing/analysis software (PicMan). For quantitative and statistical analyses of color, the newly developed software can be used for digital archive or digital forensic applications in various fields. The color differences between unrelated, similar, or identical scenes and or objects were quantified in various formats of desired color spaces such as RGB, HSV, XYZ, CIE L*a*b*, Munsell color, and hexadecimal color values. The color differences were visualized as images of pixel-by-pixel mapping of the ΔL*, Δa*, Δb*, ΔERGB, ΔEHSV, and ΔE*L*a*b* values and block comparison images of desired block sizes. Various color analyses and color-difference mapping examples using an aged and damaged oil painting before and after restoration were introduced. The effects of the image file format differences between PNG and JPG on color distortion are demonstrated by statistics and pixel-by-pixel color-difference mapping. A portrait of Chuk-ki Yoo (兪拓基, 1691–1767) on silk from the 18th century from Korea was used for further color analysis for whole and selected areas. A collector's ownership stamp of Chuk-ki Yoo stamped in red ink on the text areas in one of his book collections was extracted using the image-processing software and superimposed on the original image as a visualization enhancement example. Image analysis, processing, modification, enhancement, and highlighting, as well as statistical color analysis of digital images in most formats, can conveniently and efficiently be performed using one piece of dedicated software (PicMan). The pixel-by-pixel color information extraction and color comparison technique can be very effective for a variety of applications in art and cultural heritage objects. [ABSTRACT FROM AUTHOR]

(1) Background: angiogenesis plays an important role in the growth and metastasis of tumors. We established the CAM assay application, an image analysis software of the IKOSA platform by KML Vision, for the quantification of blood vessels with the in ovo chorioallantoic membrane (CAM) model. We added this proprietary deep learning algorithm to the already established laser speckle contrast imaging (LSCI). (2) Methods: angiosarcoma cell line tumors were grafted onto the CAM. Angiogenesis was measured at the beginning and at the end of tumor growth with both measurement methods. The CAM assay application was trained to enable the recognition of in ovo CAM vessels. Histological stains of the tissue were performed and gluconate, an anti-angiogenic substance, was applied to the tumors. (3) Results: the angiosarcoma cells formed tumors on the CAM that appeared to stay vital and proliferated. An increase in perfusion was observed using both methods. The CAM assay application was successfully established in the in ovo CAM model and anti-angiogenic effects of gluconate were observed. (4) Conclusions: the CAM assay application appears to be a useful method for the quantification of angiogenesis in the CAM model and gluconate could be a potential treatment of angiosarcomas. Both aspects should be evaluated in further research. [ABSTRACT FROM AUTHOR]

This study attempted to assess the influence of mechanical forces on potato, tapioca, wheat, rice, and maize starch granules. For this purpose, we used digital analysis of microscopic images of starch granules before and after starch grinding using ImageJ software. Additionally, we studied the influence of temperature on the size and shape of starch granules by drying the starches for 30 min at 60 °C. Our results indicate that mechanical forces very rarely cause damage to starch granules, such as breaking or cracking. In most cases, the action of mechanical forces results only in smoother shape of starch granules and their shrinking, linked with rising temperature. Results of this study show that ImageJ software can be successfully used to assess starch granule size and shape. [ABSTRACT FROM AUTHOR]

Featured Application: The algorithms described in the article can be used in any applications of image processing for recognition/segmentation of phases/morphologies, particularly in mineralogical image analysis. Their specific application field is ironmaking and corresponding optical image analysis of iron ore, sinter, and coke. Optical image analysis is commonly used to characterize different feedstock material for ironmaking, such as iron ore, iron ore sinter, coal and coke. Information is often needed for phases which have the same reflectivity and chemical composition, but different morphology. Such information is usually obtained by manual point counting, which is quite expensive and may not provide consistent results between different petrologists. To perform accurate segmentation of such phases using automated optical image analysis, the software must be able to identify specific textures. CSIRO's Carbon Steel Futures group has developed an optical image analysis software package called Mineral4/Recognition4, which incorporates a dedicated textural identification module allowing segmentation of such phases. The article discusses the problems associated with segmentation of similar phases in different ironmaking feedstock material using automated optical image analysis and demonstrates successful algorithms for textural identification. The examples cover segmentation of three different coke phases: two types of Inert Maceral Derived Components (IMDC), non-reacted and partially reacted, and Reacted Maceral Derived Components (RMDC); primary and secondary hematite in iron ore sinter; and minerals difficult to distinguish with traditional thresholding in iron ore. [ABSTRACT FROM AUTHOR]

Joint vehicle localization and categorization in high resolution aerial images can provide useful information for applications such as traffic flow structure analysis. To maintain sufficient features to recognize small-scaled vehicles, a regions with convolutional neural network features (R-CNN) -like detection structure is employed. In this setting, cascaded localization error can be averted by equally treating the negatives and differently typed positives as a multi-class classification task, but the problem of class-imbalance remains. To address this issue, a cost-effective network extension scheme is proposed. In it, the correlated convolution and connection costs during extension are reduced by feature map selection and bi-partite main-side network construction, which are realized with the assistance of a novel feature map class-importance measurement and a new class-imbalance sensitive main-side loss function. By using an image classification dataset established from a set of traditional real-colored aerial images with 0.13 m ground sampling distance which are taken from the height of 1000 m by an imaging system composed of non-metric cameras, the effectiveness of the proposed network extension is verified by comparing with its similarly shaped strong counter-parts. Experiments show an equivalent or better performance, while requiring the least parameter and memory overheads are required. [ABSTRACT FROM AUTHOR]

This study is to construct a non-contact pulse automatic positioning measurement system for Traditional Chinese Medicine (TCM) using optical triangulation measurements. The system consists of a linear laser, a CMOS image sensor and image analysis software. The linear laser is projected on the pulse beat location on the wrists; the CMOS image sensor records the process and the software analyzes the images. The program mainly uses the optical centroid and fast Fourier transform (FFT) principles to calculate centroid changes (pulse amplitude changes) from the images taken by the CMOS image sensor. It returns the positions of cun, guan and chi pulses automatically in terms of the amplitudes and the signals are then transformed from the time domain (time-amplitude) into the frequency domain (frequency-amplitude) via FFT to obtain the waveforms and frequencies of the cun, guan and chi pulses. It successfully extracts the data from the TCM pulse reading and can be a medical aid system for TCM. Combining the advantages of optical measurement and computer automation, this system provides a non-contact, easy to operate, fast in detection and low-cost equipment design. [ABSTRACT FROM AUTHOR]

The presented paper deals with the metal foams, which have a wide application potential ranging from power engineering, through catalysts to impact energy absorbers. The main aim of the paper is to propose an economical non-destructive method of determining the basic characteristics and dimensions using affordable devices. The basic principle of the proposed method lies in the image capture of metal foam and their subsequent analysis in image analysis software. An important element of the work is a comparison of results obtained by the proposed method with results obtained by high-resolution X-ray microtomography. The proposed method was evaluated in terms of measurement uncertainty and propagation of error in overall results. The use of the method is limited to the metal foams, characterized by an ordered structure, which are produced mainly by the electrophoretic deposition process. Based on the descriptive statistical analysis of results, it is possible to state, that the proposed method is in great agreement with accurate, but more expensive high-resolution X-ray microtomography. [ABSTRACT FROM AUTHOR]

In order to improve the ability of software dynamic image fault detection, a software dynamic image fault recovery path detection algorithm based on a fuzzy control algorithm is proposed. A software dynamic image fault signal model of a software dynamic image fault was constructed by adopting an embedded feature extraction and a fuzzy control algorithm, and the dynamic image fault signal of the embedded software under the multi-load was subjected to frequency spectrum decomposition and blind source separation. The method comprises the following steps: (1) carrying out noise reduction processing on a software dynamic image fault signal by adopting a multi-dimensional wavelet decomposition method, (2) carrying out wavelet entropy feature extraction on the software dynamic image fault signal of the noise reduction output, and (3) combining the wavelet structural feature recombination method to carry out the recombination of the software dynamic image fault feature. The high-order spectral characteristic of the software dynamic image fault signal was extracted and the high-order spectral characteristic of the extracted embedded software dynamic image fault recovery path was automatically matched, and the automatic identification and detection of the fault part of the software dynamic image was realized. [ABSTRACT FROM AUTHOR]

Three-dimensional (3D) cell cultures represent small avascular tumors in vitro and simulate some of the biological characteristics of solid tumors, enhancing the evaluation of anticancer drug efficacy. Automated image analysis can be used for the assessment of tumor growth and documentation of changes in the size parameters of 3D tumor spheroids following anticancer treatments such as electrochemotherapy. The objective of this article is to assess the effect of various electroporation (EP) conditions (500–750 Volts/cm, 8–20 pulses, 100 µs pulse duration, 5 Hz repetition rate) combined with different bleomycin concentrations (1–2.5 ug/mL) on normal epithelial (HCjE-Gi) and conjunctival melanoma (CRMM1, CRMM2) 3D-cell cultures, through an automated image analysis and a comparison with standard histological assays. A reduction in tumor mass with loss of cell definition was observed after ECT (750 Volts/cm with eight pulses and 500 Volts/cm with 20 pulses) with bleomycin (1 μg/mL and 2.5 μg/mL) in the histological and immunohistochemical analyses of 3D CRMM1 and CRMM2 spheroids, whereas an increase in volume and a decrease in sphericity was documented in the automated image analysis and 3D visualization of both melanoma cell lines. For all other treatment conditions and for the HCjE-Gi cell line, no significant changes to their morphological features were observed. Image analysis with integrated software tools provides an accessible and comprehensive platform for the preliminary selection of homogenous spheroids and for the monitoring of drug efficacy, implementing the traditional screening methods. [ABSTRACT FROM AUTHOR]

In this study, the ultrasonic resonance parameters of Ti6Al4V alloys under different heat treatments are measured by an impedance analyzer. The amplitude of the specimens is measured experimentally by means of optical microscope and image analysis software. These results show that the ultrasonic properties of Ti6Al4V alloys are closely related to β phase content and elastic modulus of the alloys. The highest volume fraction of the β phase appears in the specimen treated by solid solution treatment at 960 °C is 40.2%. These alloys present the lowest average elastic modulus (~99.69 GPa) and the minimum resonant frequency (55.06 kHz) and the highest average amplitude (21.48 µm) when the testing sample length is 41.25 mm. These findings can be used to guide the design of medical Ti6Al4V alloys for ultrasonic scalpels. [ABSTRACT FROM AUTHOR]

The diagenetic environment is vital in controlling reservoir quality by influencing diagenetic processes, especially porosity evolution. The Zhuhai Formation is a critical exploration target in the Huizhou Sag. However, there are considerable differences between the reservoirs in the west (Huixi) and east (Huidong) Huizhou Sag with only a 400 m difference in burial depth. To investigate causes of these differences, scanning electron microscopy (SEM), cathodoluminescence analysis, fluorescence analysis, and fluid inclusion analysis are employed for the petrological and diagenetic characterization of the target formation. Moreover, image analysis software is used to qualitatively evaluate the impacts of diagenesis on porosity. The results show that the digenetic environments in Huixi and Huidong are different. Huixi is characterized by a high content of feldspar with a stronger dissolution phenomenon than that observed in Huidong. The main cement types in Huixi are siliceous cement and kaolinite. Moreover, Huixi had a low palaeo-temperature, low palaeo-salinity, and low palaeo-pH diagenetic environment. In contrast, Huidong is accessible via deep faults and rich in lithic fragments which show visible deformation. Moreover, cements in this area include carbonate, gypsum, quartz overgrowth, kaolinite, and chlorite. This evidence confirms that the diagenetic environment in Huidong was a high palaeo-temperature and high palaeo-salinity environment with high palaeo-pH. Additionally, the palaeo-pH evolved following the sequence of weakly alkaline, acidic, alkaline and acidic. Microscopy evidence indicates that the Dongsha Uplift was a likely source of Huixi sediments during the deposition of the Zhuhai Formation. The determination of the porosity evolution shows that compaction and lithic fragment content are the main controlling factors on the reservoir quality of the Zhuhai Formation. [ABSTRACT FROM AUTHOR]

Since the 1990s, a decline of riparian black alder (Alnus glutinosa Gaertn.) has been observed over Europe. The fungus-like eukaryotic pathogen Phytophthora alni subsp. alni is thought to be a causal agent of this process; however, abiotic factors may also be involved. Previous studies suggest that climate conditions and, especially, depletion of groundwater level may be among the most important factors that trigger this phenomenon. We investigated the radial growth and wood vessel diameter of black alder trees of various vigour classes as well as their response to groundwater level changes to search for the link between soil water resources availability and mortality related to alder dieback. Samples were collected in the natural stand located near Sieraków village in the Kampinoski National Park, central Poland, in the area where alder dieback has been recently observed. Based on the crown defoliation level, three vigour classes (healthy, weakened, and dead trees) were distinguished. Cross sections were prepared with a sliding microtome, and Cell P image analysis software was used for the measurements. Tree-ring width (TRW) and vessel diameter (VD) were determined and correlated with the monthly values of precipitation and groundwater level. Alders of the analysed vigour classes exhibited similar patterns of TRW and VD changes over the analysis time. The narrowest tree rings were observed in weakened alders, while the largest vessels were noted in healthy trees. In the case of TRW and VD chronologies, the weakest, and hence insignificant, resemblance was found for healthy and dead trees. TRW and VD of the analysed alders were not correlated with the monthly sum of precipitation, but a negative influence of rainfall in April was observed. In turn, groundwater level had an impact on the radial growth and wood anatomical features of the analysed trees. A negative effect of the highest water table level was found for TRW of weakened and dead trees as well as for VD of healthy and weakened alders. The lowest groundwater level and the amplitude of the water table positively affected VD of the dead trees. Alder decline has a polyetiological nature, and groundwater level fluctuations are one of many factors contributing to disease development. [ABSTRACT FROM AUTHOR]

Detecting small amounts of analyte in clinical practice is challenging because of deficiencies in specimen sample availability and unsuitable sampling environments that prevent reliable sampling. Paper-based analytical devices (PADs) have successfully been used to detect ultralow amounts of analyte, and origami-based PADs (O-PADs) offer advantages that may boost the overall potential of PADs in general. In this study, we investigated two potential clinical applications for O-PADs. The first O-PAD we investigated was an origami-based enzyme-linked immunosorbent assay (ELISA) system designed to detect different concentrations of rabbit IgG. This device was designed with four wing structures, each of which acted as a reagent loading zone for pre-loading ELISA reagents, and a central test sample loading zone. Because this device has a low limit of detection (LOD), it may be suitable for detecting IgG levels in tears from patients with a suspected viral infection (such as herpes simplex virus (HSV)). The second O-PAD we investigated was designed to detect paraquat levels to determine potential poisoning. To use this device, we sequentially folded each of two separate reagent zones, one preloaded with NaOH and one preloaded with ascorbic acid (AA), over the central test zone, and added 8 µL of sample that then flowed through each reagent zone and onto the central test zone. The device was then unfolded to read the results on the test zone. The three folded layers of paper provided a moist environment not achievable with conventional paper-based ELISA. Both O-PADs were convenient to use because reagents were preloaded, and results could be observed and analyzed with image analysis software. O-PADs expand the testing capacity of simpler PADs while leveraging their characteristic advantages of convenience, cost, and ease of use, particularly for point-of-care diagnosis. [ABSTRACT FROM AUTHOR]

Sandstones and many carbonates (e.g., oolitic limestone and other grainstones), comprise solid particulates (grains) and pores, which have a given pore network architecture relationship, and associated porosity—permeability values. Over time, through the process of diagenesis, the pore network architecture may be extensively altered. Changes can include compaction, particle deformation, cementation, dissolution and fracturing, with the pathway followed after deposition depending on factors such as the energy level, rate of burial, degree of biological activity, local heat flow, sediment composition, Eh, pH and the presence or absence of organic materials. Any method that provides a means of modelling changes is therefore highly desirable, in particular, allowing a prediction of changes in porosity and permeability with time. The current work illustrates a simple method that uses freely available open source image analysis software to model the development of cement phases within an oolitic limestone in three-dimensions. As well as cementation, it demonstrates the modelling of fracture development and dissolution processes, and records how porosity and permeability change during such processes. [ABSTRACT FROM AUTHOR]

Background: Autofluorescence imaging (AFI) is useful for diagnosing colon neoplasms, but what affects the AFI intensity remains unclear. This study investigated the association between AFI and the histological characteristics, aberrant methylation status, and aberrant expression in colon neoplasms. Methods: Fifty-three patients with colorectal neoplasms who underwent AFI were enrolled. The AFI intensity (F index) was compared with the pathological findings and gene alterations. The F index was calculated using an image analysis software program. The pathological findings were assessed by the tumor crypt density, cell densities, and N/C ratio. The aberrant methylation of p16, E-cadherin, Apc, Runx3, and hMLH1 genes was determined by a methylation-specific polymerase chain reaction. The aberrant expression of p53 and Ki-67 was evaluated by immunohistochemical staining. Results: An increased N/C ratio, the aberrant expression of p53, Ki-67, and the altered methylation of p16 went together with a lower F index. The other pathological findings and the methylation status showed no association with the F index. Conclusions: AFI reflects the nuclear enlargement of tumor cells, the cell proliferation ability, and the altered status of cell proliferation-related genes, indicating that AFI is a useful and practical method for predicting the dysplastic grade of tumor cells and cell proliferation. [ABSTRACT FROM AUTHOR]

This paper describes a method of laser ablation for improving the hydrophobic properties of vulcanized rubber. The treatment was tested on acrylonitrile rubber (NBR) and styrene butadiene rubber (SBR) containing carbon nanotubes and soot as fillers. The surface layer of the vulcanizates was modified using a nanosecond-pulsed laser at 1060 nm wavelength. The parameters of the ablation process were congruent, so no chemical changes in the polymeric material were observed. Evaluation of the surface condition of the laser-textured samples was performed using a Leica MZ6 stereoscopic microscope, operating with MultiScan 8.0 image analysis software. The contact angles were determined for all the samples before and after the surface modification process. Following modification of the surface morphology, with the best parameters of laser ablation, the contact angle increased, reaching 147°, which is very close to the threshold of superhydrophobicity (150°). On the basis of the results from several tests, laser ablation with a fiber-pulsed laser can be considered a very useful method for producing rubbers with superhydrophobic surfaces. [ABSTRACT FROM AUTHOR]