Morphology-Guided Graph Search for Untangling Objects: C. elegans Analysis

Raviv, Tammy Riklin; Ljosa, Vebjorn; Conery, Annie L.; Ausubelc, F. M.; Carpenter, Anne E.; Golland, Polina; Wählby, Carolina

doi:10.1007/978-3-642-15711-0_79

Cited by 14 publications

(7 citation statements)

References 15 publications

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“…For example, the current implementation of WormScan requires non-overlapping nematodes for effective image analysis, which is achieved by limiting worm density to less than 150 individuals on a 5.5 cm diameter plate. However, worms can be digitally untangled, which could allow a higher density of worms per plate to be analyzed in future studies [49] . Furthermore, ImageJ was adapted to allow WormScan to observe similar sized species.…”

Section: Discussionmentioning

confidence: 99%

WormScan: A Technique for High-Throughput Phenotypic Analysis of Caenorhabditis elegans

2012

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BackgroundThere are four main phenotypes that are assessed in whole organism studies of Caenorhabditis elegans; mortality, movement, fecundity and size. Procedures have been developed that focus on the digital analysis of some, but not all of these phenotypes and may be limited by expense and limited throughput. We have developed WormScan, an automated image acquisition system that allows quantitative analysis of each of these four phenotypes on standard NGM plates seeded with E. coli. This system is very easy to implement and has the capacity to be used in high-throughput analysis.Methodology/Principal FindingsOur system employs a readily available consumer grade flatbed scanner. The method uses light stimulus from the scanner rather than physical stimulus to induce movement. With two sequential scans it is possible to quantify the induced phototactic response. To demonstrate the utility of the method, we measured the phenotypic response of C. elegans to phosphine gas exposure. We found that stimulation of movement by the light of the scanner was equivalent to physical stimulation for the determination of mortality. WormScan also provided a quantitative assessment of health for the survivors. Habituation from light stimulation of continuous scans was similar to habituation caused by physical stimulus.Conclusions/SignificanceThere are existing systems for the automated phenotypic data collection of C. elegans. The specific advantages of our method over existing systems are high-throughput assessment of a greater range of phenotypic endpoints including determination of mortality and quantification of the mobility of survivors. Our system is also inexpensive and very easy to implement. Even though we have focused on demonstrating the usefulness of WormScan in toxicology, it can be used in a wide range of additional C. elegans studies including lifespan determination, development, pathology and behavior. Moreover, we have even adapted the method to study other species of similar dimensions.

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Section: Discussionmentioning

confidence: 99%

WormScan: A Technique for High-Throughput Phenotypic Analysis of Caenorhabditis elegans

2012

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“…It is also relatively easy to incorporate continuous object-level regularization into level sets, such as shape priors. Another type of energy-based model is based on graph search [16,17], graph cuts [18,19] or normalized cuts [20]. Such methods attempt to derive the segmentation with global constraints, using well-defined graphical structures to represent the spatial relationships between regions.…”

Section: Introductionmentioning

confidence: 99%

Region-based progressive localization of cell nuclei in microscopic images with data adaptive modeling

et al. 2013

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BackgroundSegmenting cell nuclei in microscopic images has become one of the most important routines in modern biological applications. With the vast amount of data, automatic localization, i.e. detection and segmentation, of cell nuclei is highly desirable compared to time-consuming manual processes. However, automated segmentation is challenging due to large intensity inhomogeneities in the cell nuclei and the background.ResultsWe present a new method for automated progressive localization of cell nuclei using data-adaptive models that can better handle the inhomogeneity problem. We perform localization in a three-stage approach: first identify all interest regions with contrast-enhanced salient region detection, then process the clusters to identify true cell nuclei with probability estimation via feature-distance profiles of reference regions, and finally refine the contours of detected regions with regional contrast-based graphical model. The proposed region-based progressive localization (RPL) method is evaluated on three different datasets, with the first two containing grayscale images, and the third one comprising of color images with cytoplasm in addition to cell nuclei. We demonstrate performance improvement over the state-of-the-art. For example, compared to the second best approach, on the first dataset, our method achieves 2.8 and 3.7 reduction in Hausdorff distance and false negatives; on the second dataset that has larger intensity inhomogeneity, our method achieves 5% increase in Dice coefficient and Rand index; on the third dataset, our method achieves 4% increase in object-level accuracy.ConclusionsTo tackle the intensity inhomogeneities in cell nuclei and background, a region-based progressive localization method is proposed for cell nuclei localization in fluorescence microscopy images. The RPL method is demonstrated highly effective on three different public datasets, with on average 3.5% and 7% improvement of region- and contour-based segmentation performance over the state-of-the-art.

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“…These practices include mandatory duties, for executions where one is rewarded by God for doing, and subject to God's punishment for failing to perform (e.g. five-time prayer), and some recommend the voluntary practice, in which a person is rewarded for doing so, but is not punished for not performing (e.g., voluntary prayer, voluntary charity, and the like) (Albelaikhi, 1997). Beliefs and practices can be considered the two most important components of a slam religion.…”

Section: Religious Charactersmentioning

confidence: 99%

“…People are expected to be led by their attitudes and actions on it, and that's how attitudes can be a good indicator of religiosity. The fourth component (knowledge) is considered and the item is written measuring the level of general knowledge a person has about an Islamic religion (Albelaikhi, 1997).…”

Section: Religious Charactersmentioning

confidence: 99%

Implementing Religious Characters of Early Children in the Pandemic Time of Covid 19

Lestari

Yufiarti

Supena

2020

IJMMU

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The purpose of this study is to provide insight into the implementation of religious character planting in early childhood in the family during the COVID-19 pandemic. The study involved 10 parents. The results of research on the COVID-19 pandemic make families spend more time with children. There are four aspects of religious character instilled in the family namely beliefs, practices, attitudes, and knowledge. In implementing religious characters there are several methods that parents use to embed every aspect of a religious character. Methods of lectures and storytelling to instill aspects of beliefs, methods of lectures, and direct practice in aspects of attitude and practice. Methods of storytelling and dialogue in instilling religious character knowledge in early childhood.

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Morphology-Guided Graph Search for Untangling Objects: C. elegans Analysis

Cited by 14 publications

References 15 publications

WormScan: A Technique for High-Throughput Phenotypic Analysis of Caenorhabditis elegans

WormScan: A Technique for High-Throughput Phenotypic Analysis of Caenorhabditis elegans

Region-based progressive localization of cell nuclei in microscopic images with data adaptive modeling

Implementing Religious Characters of Early Children in the Pandemic Time of Covid 19

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