Definiens Developer Research Articles

Automated Image Analysis of the Host-Pathogen Interaction between Phagocytes and Aspergillus fumigatus

Aspergillus fumigatus is a ubiquitous airborne fungus and opportunistic human pathogen. In immunocompromised hosts, the fungus can cause life-threatening diseases like invasive pulmonary aspergillosis. Since the incidence of fungal systemic infections drastically increased over the last years, it is a major goal to investigate the pathobiology of A. fumigatus and in particular the interactions of A. fumigatus conidia with immune cells. Many of these studies include the activity of immune effector cells, in particular of macrophages, when they are confronted with conidia of A. fumigus wild-type and mutant strains. Here, we report the development of an automated analysis of confocal laser scanning microscopy images from macrophages coincubated with different A. fumigatus strains. At present, microscopy images are often analysed manually, including cell counting and determination of interrelations between cells, which is very time consuming and error-prone. Automation of this process overcomes these disadvantages and standardises the analysis, which is a prerequisite for further systems biological studies including mathematical modeling of the infection process. For this purpose, the cells in our experimental setup were differentially stained and monitored by confocal laser scanning microscopy. To perform the image analysis in an automatic fashion, we developed a ruleset that is generally applicable to phagocytosis assays and in the present case was processed by the software Definiens Developer XD. As a result of a complete image analysis we obtained features such as size, shape, number of cells and cell-cell contacts. The analysis reported here, reveals that different mutants of A. fumigatus have a major influence on the ability of macrophages to adhere and to phagocytose the respective conidia. In particular, we observe that the phagocytosis ratio and the aggregation behaviour of pksP mutant compared to wild-type conidia are both significantly increased.

An object-oriented approach to automated landform mapping: A case study of drumlins

This paper details an automated object-oriented approach to mapping landforms from digital elevation models (DEMs), using the example of drumlins in the Chautauqua drumlin field in NW Pennsylvania and upstate New York. Object-oriented classification is highly desirable as it can identify specific shapes in datasets based on both the pixel values in a raster dataset and the contextual information between pixels and extracted objects. The methodology is built specifically for application to the USGS 30 m resolution DEM data, which are freely available to the public and of sufficient resolution to map medium scale landforms. Using the raw DEM data, as well as derived aspect and slope, Definiens Developer (v.7) was used to perform multiresolution segmentation, followed by rule-based classification in order to extract individual polygons that represent drumlins. Drumlins obtained by automated extraction were visually and statistically compared to those identified via manual digitization. Detailed morphometric descriptive statistics such as means, ranges, and standard deviations were inspected and compared for length, width, elongation ratio, area, and perimeter. Although the manual and automated results were not always statistically identical, a more detailed comparison of just the drumlins identified by both procedures showed that the automated methods easily matched the manual digitization. Differences in the two methods related to mapping compound drumlins, and smaller and larger drumlins. The automated method generally identified more features in these categories than the manual method and thus outperformed the manual method.

A Novel Texture-Preceded Segmentation Algorithm for High-Resolution Imagery

Image segmentation is crucial to object-oriented remote sensing imagery analysis. In this paper, a novel texture-preceded segmentation algorithm is proposed for high-resolution remote sensing imagery, in which texture clustering is first carried out as a loose constraint for later segmentation. The algorithm is based on the graph models of region adjacency graph and nearest neighbor graph, which can achieve fast node merging, depending on the global optimum. Here, a combined distance, composed of texture, spectral, and shape features, is established to measure the similarity between nodes and gives the same semantic descriptions for the texture objects. Then, the combined distance is applied to graph models, and the final segmentation result can be obtained iteratively by fast merging. During the merging process, optimal sequence merging interacts with texture clustering to refine the real edges of a texture region. This algorithm cannot only merge the homogeneous texture segments with spectral variability easily but can also detect the real object boundaries well. The experiments on high-resolution imagery show that, in terms of the same number of segments, the proposed algorithm can improve segmentation accuracy by 10%-20% compared to the results obtained by pure spectral features with Definiens Developer software.

Development of automated imaging and analysis for zebrafish chemical screens.

We demonstrate the application of image-based high-content screening (HCS) methodology to identify small molecules that can modulate the FGF/RAS/MAPK pathway in zebrafish embryos. The zebrafish embryo is an ideal system for in vivo high-content chemical screens. The 1-day old embryo is approximately 1mm in diameter and can be easily arrayed into 96-well plates, a standard format for high throughput screening. During the first day of development, embryos are transparent with most of the major organs present, thus enabling visualization of tissue formation during embryogenesis. The complete automation of zebrafish chemical screens is still a challenge, however, particularly in the development of automated image acquisition and analysis. We previously generated a transgenic reporter line that expresses green fluorescent protein (GFP) under the control of FGF activity and demonstrated their utility in chemical screens 1. To establish methodology for high throughput whole organism screens, we developed a system for automated imaging and analysis of zebrafish embryos at 24-48 hours post fertilization (hpf) in 96-well plates 2. In this video we highlight the procedures for arraying transgenic embryos into multiwell plates at 24hpf and the addition of a small molecule (BCI) that hyperactivates FGF signaling 3. The plates are incubated for 6 hours followed by the addition of tricaine to anesthetize larvae prior to automated imaging on a Molecular Devices ImageXpress Ultra laser scanning confocal HCS reader. Images are processed by Definiens Developer software using a Cognition Network Technology algorithm that we developed to detect and quantify expression of GFP in the heads of transgenic embryos. In this example we highlight the ability of the algorithm to measure dose-dependent effects of BCI on GFP reporter gene expression in treated embryos.

Development of automated imaging and analysis for zebrafish chemical screens.

We demonstrate the application of image-based high-content screening (HCS) methodology to identify small molecules that can modulate the FGF/RAS/MAPK pathway in zebrafish embryos. The zebrafish embryo is an ideal system for in vivo high-content chemical screens. The 1-day old embryo is approximately 1mm in diameter and can be easily arrayed into 96-well plates, a standard format for high throughput screening. During the first day of development, embryos are transparent with most of the major organs present, thus enabling visualization of tissue formation during embryogenesis. The complete automation of zebrafish chemical screens is still a challenge, however, particularly in the development of automated image acquisition and analysis. We previously generated a transgenic reporter line that expresses green fluorescent protein (GFP) under the control of FGF activity and demonstrated their utility in chemical screens 1. To establish methodology for high throughput whole organism screens, we developed a system for automated imaging and analysis of zebrafish embryos at 24-48 hours post fertilization (hpf) in 96-well plates 2. In this video we highlight the procedures for arraying transgenic embryos into multiwell plates at 24hpf and the addition of a small molecule (BCI) that hyperactivates FGF signaling 3. The plates are incubated for 6 hours followed by the addition of tricaine to anesthetize larvae prior to automated imaging on a Molecular Devices ImageXpress Ultra laser scanning confocal HCS reader. Images are processed by Definiens Developer software using a Cognition Network Technology algorithm that we developed to detect and quantify expression of GFP in the heads of transgenic embryos. In this example we highlight the ability of the algorithm to measure dose-dependent effects of BCI on GFP reporter gene expression in treated embryos.

Analysis on spatial structure of landuse change based on remote sensing and geographical information system

Analyzing spatio-temporal characteristics of landuse cover change is essential for understanding the pattern of urbanization. More importantly, such analysis can provide much information for decision-making. Landuse changed rapidly in Guangzhou in the last several years, so that it is necessary to study the spatial structure of landuse change. DOM (Digital Orthophoto Map) of Guangzhou in 2003, 2005 are acquired for this study. Accurate landuse information was first extracted by Definiens Developer. Secondly, we applied the landuse transfer model to analyze the mutual conversions among different landuse classes. Thirdly, a landuse spatial position conversion and quantity change model was established to analyze the position conversion of landuse classes from a quantitative perspective. Finally, Landuse dynamicity model is applied to study Guangzhou's landuse change level and the reasons of the change are analyzed. The results showed that farmland diminished relatively fast and adjustable landuse areas increased substantially. The main reason for farmland reduction lies in that part of the original farmland has been turned into other cultivated lands. The absolute quantity of landuse change is enormous, dominated by the internal conversion among landuse categories, such as farmland converted into garden and other types of cultivated lands.

ESP: a tool to estimate scale parameter for multiresolution image segmentation of remotely sensed data

The spatial resolution of imaging sensors has increased dramatically in recent years, and so too have the challenges associated with extracting meaningful information from their data products. Object-based image analysis (OBIA) is gaining rapid popularity in remote sensing science as a means of bridging very high spatial resolution (VHSR) imagery and GIS. Multiscalar image segmentation is a fundamental step in OBIA, yet there is currently no tool available to objectively guide the selection of appropriate scales for segmentation. We present a technique for estimating the scale parameter in image segmentation of remotely sensed data with Definiens Developer®. The degree of heterogeneity within an image-object is controlled by a subjective measure called the ‘scale parameter’, as implemented in the mentioned software. We propose a tool, called estimation of scale parameter (ESP), that builds on the idea of local variance (LV) of object heterogeneity within a scene. The ESP tool iteratively generates image-objects at multiple scale levels in a bottom-up approach and calculates the LV for each scale. Variation in heterogeneity is explored by evaluating LV plotted against the corresponding scale. The thresholds in rates of change of LV (ROC-LV) indicate the scale levels at which the image can be segmented in the most appropriate manner, relative to the data properties at the scene level. Our tests on different types of imagery indicated fast processing times and accurate results. The simple yet robust ESP tool enables fast and objective parametrization when performing image segmentation and holds great potential for OBIA applications.

An Evaluation of Object-Oriented Image Analysis Techniques to Identify Motorized Vehicle Effects in Semi-arid to Arid Ecosystems of the American West

Human disturbance is a leading ecosystem stressor. Human-induced modifications include transportation networks, areal disturbances due to resource extraction, and recreation activities. High-resolution imagery and object-oriented classification rather than pixel-based techniques have successfully identified roads, buildings, and other anthropogenic features. Three commercial, automated feature-extraction software packages (Visual Learning Systems' Feature Analyst, ENVI Feature Extraction, and Definiens Developer) were evaluated by comparing their ability to effectively detect the disturbed surface patterns from motorized vehicle traffic. Each package achieved overall accuracies in the 70% range, demonstrating the potential to map the surface patterns. The Definiens classification was more consistent and statistically valid.

Improvement of Image Segmentation Accuracy Based on Multiscale Optimization Procedure

This letter proposes an optimization approach that enhances the quality of image segmentation using the software Definiens Developer. The procedure aims at the minimization of over- and undersegmentations in order to attain more accurate segmentation results. The optimization iteratively combines a sequence of multiscale segmentation, feature-based classification, and classification-based object refinement. The developed method has been applied to various remotely sensed data and is compared to the results achieved with the established segmentation procedures provided by the Definiens Developer software. The quantitative assessment of segmentation accuracy based on reference objects is derived from an aerial image, and a high-resolution synthetic aperture radar scene shows an improvement of 20%-40% in object accuracy by applying the proposed procedure.