A Feature Set for Cytometry on Digitized Microscopic Images

Rodenacker, Karsten; Bengtsson, Ewert

doi:10.1155/2003/548678

Cited by 187 publications

(115 citation statements)

References 66 publications

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“…In Boland and Murphy (2001) a standard feature set for subcellular location characterization was introduced and extended to a large set of 2D and 3D image features (Huang and Murphy 2004). Also in other fields of microscopy image classification, a wide range of image features has been studied (e.g., Ronneberger et al 2002;Lindblad et al 2003;Rodenacker and Bengtsson 2003;Pincus et al 2007). A general overview of commonly used image feature types is given, e.g., Theodoridis and Koutroumbas (1999).…”

Section: Feature Extractionmentioning

confidence: 99%

Automatic analysis of dividing cells in live cell movies to detect mitotic delays and correlate phenotypes in time

Harder¹,

Mora-Bermúdez²,

Godinez

et al. 2009

Genome Res.

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Live-cell imaging allows detailed dynamic cellular phenotyping for cell biology and, in combination with small molecule or drug libraries, for high-content screening. Fully automated analysis of live cell movies has been hampered by the lack of computational approaches that allow tracking and recognition of individual cell fates over time in a precise manner. Here, we present a fully automated approach to analyze time-lapse movies of dividing cells. Our method dynamically categorizes cells into seven phases of the cell cycle and five aberrant morphological phenotypes over time. It reliably tracks cells and their progeny and can thus measure the length of mitotic phases and detect cause and effect if mitosis goes awry. We applied our computational scheme to annotate mitotic phenotypes induced by RNAi gene knockdown of CKAP5 (also known as ch-TOG) or by treatment with the drug nocodazole. Our approach can be readily applied to comparable assays aiming at uncovering the dynamic cause of cell division phenotypes.[Supplemental material is available online at http://www.genome.org.]High-content image-based screening is a powerful technology for gene function studies or drug profiling. This technology is characterized by the combination of automated microscopy to rapidly acquire high-content images of treated cells and sophisticated computational methods to extract quantitative information in an automatic and unbiased way.Quantitative studies have been performed based on populations of cells to analyze high-throughput RNAi (Wheeler et al. 2004;Neumann et al. 2006;Goshima et al. 2007), protein overexpression (Harada et al. 2005), or drug profiling screens (Perlman et al. 2004;Loo et al. 2007). Such studies require methods for segmentation and feature extraction, and classification if different object classes are considered. Publicly available software platforms like CellProfiler (Carpenter et al. 2006) can be applied. For population-based studies, however, results are often limited to general features of entire cell populations at certain time points.By contrast, following single cells over time allows studying the inherent dynamics of cellular and molecular processes more accurately and is consequently widely used in state-of-the-art cell biology. To make time-lapse imaging of single cells applicable for high content screening, additional methods for tracking of cells throughout image sequences and recognition of their phenotypic changes are required. Tracking approaches have been used, e.g., to quantify the level of fluorescently tagged proteins over time (e.g., Sigal et al. 2006; or to quantify cell-cell interactions and cell migration dynamics (e.g., Chen et al. 2009).Automated classification methods have also been used on static images to distinguish different phenotype classes, providing information on the structure and location of subcellular phenotypes at a single cell level (e.g., Conrad et al. 2004;Huang and Murphy 2004;Chen et al. 2007;Hamilton et al. 2007).Combining classification and tracking methods to stu...

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Section: Feature Extractionmentioning

confidence: 99%

Automatic analysis of dividing cells in live cell movies to detect mitotic delays and correlate phenotypes in time

Harder¹,

Mora-Bermúdez²,

Godinez

et al. 2009

Genome Res.

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“…It has been proven in many studies that chromatin distribution corresponds to the state of malignancy. Two basic approaches to analysis of a chromatin constitution are known [9]. Within the first, structural, the chromatin distribution is considered as a local arrangement of rather small objects of varying intensity.…”

Section: Properties Of Cell Images and Requirements To The Methodsmentioning

confidence: 99%

“…The main disadvantage of known textural methods [9] is their sensitivity parameters and conditions of image acquisition, to properties of researched preparations, and also to precision of microscope focusing.…”

Section: Properties Of Cell Images and Requirements To The Methodsmentioning

confidence: 99%

A Technique for Extraction of Diagnostic Data from Cytological Specimens

Gurevich

Khilkov

Murashov

2003

Lecture Notes in Computer Science

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Abstract. In this paper, a possibility of developing a new criterion for diagnostics of hematopoietic tumors, such as chronic B-cell lymphatic leukemia, transformation of chronic B-cell lymphatic leukemia into lymphosarcoma, and primary B-cell lymphosarcoma, from images of cell nuclei of lymphatic nodes is considered. A method for image analysis of lymphatic node specimens is developed on the basis of the scale space approach. A diagnostically important criterion is defined as a total amount of points of spatial intensity extrema in the families of blurred images generated by the given image of a cell nucleus. The procedure for calculating criterion values is presented.

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“…The existing techniques based on digital microscopy [13][14][15][16] , however, are time-consuming and resource-demanding, as images are typically captured for the entire sample area, or even through three-dimensional space [17][18][19][20] , followed by stitching and processing to identify and quantitate targets of interest. Their quantification is also less accurate, because different types of noise and background emission interfere in the measurement of absolute intensities, and targets that are randomly located at the periphery of the field-of-view (FOV) have large variation in excitation and detection efficiencies [21][22][23] . The key to realising a simplified accessible technique for quantitative luminescence measurements lies in the improvements in both the signal-to-background contrast and the pinpointing precision with which each target is brought to the centre of the FOV.…”

Section: Introductionmentioning

confidence: 99%

High-Precision Pinpointing of Luminescent Targets in Encoder-Assisted Scanning Microscopy Allowing High-Speed Quantitative Analysis

Zheng

Zhao

et al. 2015

Anal. Chem.

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The new agreement specifically addresses what authors can do with different versions of their manuscript -e.g. use in theses and collections, teaching and training, conference presentations, sharing with colleagues, and posting on websites and repositories. The terms under which these uses can occur are clearly identified to prevent misunderstandings that could jeopardize final publication of a manuscript (Section II, Permitted Uses by Authors). Easy Reference User Guide Posting Submitted Works on Websites and Repositories:A digital file of the unedited manuscript version of a Submitted Work may be made publicly available on websites or repositories (e.g. the Author's personal website, preprint servers, university networks or primary employer's institutional websites, third party institutional or subject-based repositories, and conference websites that feature presentations by the Author(s) based on the Submitted Work) under the following conditions:• The posting must be for non-commercial purposes and not violate the ACS' "Ethical Guidelines to Publication of Chemical Research" (see http://pubs.acs.org/ethics).• If the Submitted Work is accepted for publication in an ACS journal, then the following notice should be included at the time of posting, or the posting amended as appropriate: "This document is the unedited Author's version of a Submitted Work that was subsequently accepted for publication in [JournalTitle], copyright © American Chemical Society after peer review. To access the final edited and published work see [insert ACS Articles on Request author-directed link to Published Work, see http://pubs.acs.org/page/policy/articlesonrequest/index.html]." Note: It is the responsibility of the Author(s) to confirm with the appropriate ACS journal editor that the timing of the posting of the Submitted Work does not conflict with journal prior publication/embargo policies (see http://pubs.acs.org/page/policy/prior/index.html)If any prospective posting of the Submitted Work, whether voluntary or mandated by the Author(s)' funding agency, primary employer, or, in the case of Author(s) employed in academia, university administration, would violate any of the above conditions, the Submitted Work may not be posted. In these cases, Author(s) may either sponsor the immediate public availability of the final Published Work through participation in the feebased ACS AuthorChoice program (for information about this program see http://pubs.acs.org/page/policy/authorchoice/index.html) or, if applicable, seek a waiver from the relevant institutional policy. July, 2016 ABSTRACTCompared with routine microscopy imaging of a few analytes at a time, rapid scanning through the whole sample area of a microscope slide to locate every single target object offers many advantages in terms of simplicity, speed, throughput, and potential for robust quantitative analysis. Existing techniques that accommodate solid-phase samples incorporating individual micron-sized targets generally rely on digital microscopy and image analysis, with in...

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A Feature Set for Cytometry on Digitized Microscopic Images

Cited by 187 publications

References 66 publications

Automatic analysis of dividing cells in live cell movies to detect mitotic delays and correlate phenotypes in time

Automatic analysis of dividing cells in live cell movies to detect mitotic delays and correlate phenotypes in time

A Technique for Extraction of Diagnostic Data from Cytological Specimens

High-Precision Pinpointing of Luminescent Targets in Encoder-Assisted Scanning Microscopy Allowing High-Speed Quantitative Analysis

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