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Literature DB >> 22743771

A call for bioimaging software usability.

Anne E Carpenter¹, Lee Kamentsky, Kevin W Eliceiri.

Abstract

Bioimaging software developed in a research setting often is not widely used by the scientific community. We suggest that, to maximize both the public's and researchers' investments, usability should be a more highly valued goal. We describe specific characteristics of usability toward which bioimaging software projects should aim.

Entities: Chemical Disease Gene

Mesh：

Year: 2012 PMID： 22743771 PMCID： PMC3641581 DOI： 10.1038/nmeth.2073

Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547

16 in total

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2. The case for open computer programs.

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3. Better bioinformatics through usability analysis.

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4. NIH Image to ImageJ: 25 years of image analysis.

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5. The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging.

Authors: Ilya G Goldberg; Chris Allan; Jean-Marie Burel; Doug Creager; Andrea Falconi; Harry Hochheiser; Josiah Johnston; Jeff Mellen; Peter K Sorger; Jason R Swedlow
Journal: Genome Biol Date: 2005-05-03 Impact factor: 13.583

6. Metadata matters: access to image data in the real world.

Authors: Melissa Linkert; Curtis T Rueden; Chris Allan; Jean-Marie Burel; Will Moore; Andrew Patterson; Brian Loranger; Josh Moore; Carlos Neves; Donald Macdonald; Aleksandra Tarkowska; Caitlin Sticco; Emma Hill; Mike Rossner; Kevin W Eliceiri; Jason R Swedlow
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7. Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images.

Authors: Pekka Ruusuvuori; Tarmo Aijö; Sharif Chowdhury; Cecilia Garmendia-Torres; Jyrki Selinummi; Mirko Birbaumer; Aimée M Dudley; Lucas Pelkmans; Olli Yli-Harja
Journal: BMC Bioinformatics Date: 2010-05-13 Impact factor: 3.169

8. Persistence and availability of Web services in computational biology.

Authors: Sebastian J Schultheiss; Marc-Christian Münch; Gergana D Andreeva; Gunnar Rätsch
Journal: PLoS One Date: 2011-09-22 Impact factor: 3.240

9. Scientific software development is not an oxymoron.

Authors: Susan M Baxter; Steven W Day; Jacquelyn S Fetrow; Stephanie J Reisinger
Journal: PLoS Comput Biol Date: 2006-09-08 Impact factor: 4.475

10. Computational biology resources lack persistence and usability.

Authors: Stella Veretnik; J Lynn Fink; Philip E Bourne
Journal: PLoS Comput Biol Date: 2008-07-18 Impact factor: 4.475

50 in total

1. A call for bioimaging software usability.

Authors: Anne E Carpenter; Lee Kamentsky; Kevin W Eliceiri
Journal: Nat Methods Date: 2012-06-28 Impact factor: 28.547

2. Quantitative evaluation of software packages for single-molecule localization microscopy.

Authors: Daniel Sage; Hagai Kirshner; Thomas Pengo; Nico Stuurman; Junhong Min; Suliana Manley; Michael Unser
Journal: Nat Methods Date: 2015-06-15 Impact factor: 28.547

3. Leveraging Terminology Services for Extract-Transform-Load Processes: A User-Centered Approach.

Authors: Kevin J Peterson; Guoqian Jiang; Scott M Brue; Hongfang Liu
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4. Imagining the future of bioimage analysis.

Authors: Erik Meijering; Anne E Carpenter; Hanchuan Peng; Fred A Hamprecht; Jean-Christophe Olivo-Marin
Journal: Nat Biotechnol Date: 2016-12-07 Impact factor: 54.908

5. Biological imaging software tools.

Authors: Kevin W Eliceiri; Michael R Berthold; Ilya G Goldberg; Luis Ibáñez; B S Manjunath; Maryann E Martone; Robert F Murphy; Hanchuan Peng; Anne L Plant; Badrinath Roysam; Nico Stuurman; Nico Stuurmann; Jason R Swedlow; Pavel Tomancak; Anne E Carpenter
Journal: Nat Methods Date: 2012-06-28 Impact factor: 28.547

6. Software tools for single-cell tracking and quantification of cellular and molecular properties.

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Journal: Nat Biotechnol Date: 2016-07-12 Impact factor: 54.908

Review 7. Challenges in long-term imaging and quantification of single-cell dynamics.

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Review 8. Robust Nucleus/Cell Detection and Segmentation in Digital Pathology and Microscopy Images: A Comprehensive Review.

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Journal: IEEE Rev Biomed Eng Date: 2016-01-06

9. ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis.

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Review 10. Harnessing non-destructive 3D pathology.

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Journal: Nat Biomed Eng Date: 2021-02-15 Impact factor: 25.671