Dataset Information

Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software.

ABSTRACT:

Unlabelled

There is a strong and growing need in the biology research community for accurate, automated image analysis. Here, we describe CellProfiler 2.0, which has been engineered to meet the needs of its growing user base. It is more robust and user friendly, with new algorithms and features to facilitate high-throughput work. ImageJ plugins can now be run within a CellProfiler pipeline.

Availability and implementation

CellProfiler 2.0 is free and open source, available at http://www.cellprofiler.org under the GPL v. 2 license. It is available as a packaged application for Macintosh OS X and Microsoft Windows and can be compiled for Linux.

Contact

anne@broadinstitute.org

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Kamentsky L

PROVIDER: S-EPMC3072555 | biostudies-literature | 2011 Apr

REPOSITORIES: biostudies-literature

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Publications

Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software.

Kamentsky Lee L Jones Thouis R TR Fraser Adam A Bray Mark-Anthony MA Logan David J DJ Madden Katherine L KL Ljosa Vebjorn V Rueden Curtis C Eliceiri Kevin W KW Carpenter Anne E AE

Bioinformatics (Oxford, England) 20110223 8

<h4>Unlabelled</h4>There is a strong and growing need in the biology research community for accurate, automated image analysis. Here, we describe CellProfiler 2.0, which has been engineered to meet the needs of its growing user base. It is more robust and user friendly, with new algorithms and features to facilitate high-throughput work. ImageJ plugins can now be run within a CellProfiler pipeline.<h4>Availability and implementation</h4>CellProfiler 2.0 is free and open source, available at http ...[more]

PMID: 21349861

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Project description:BackgroundMaize (Zea mays L.) is one of the most important food sources in the world and has been one of the main targets of plant genetics and phenotypic research for centuries. Observation and analysis of various morphological phenotypic traits during maize growth are essential for genetic and breeding study. The generally huge number of samples produce an enormous amount of high-resolution image data. While high throughput plant phenotyping platforms are increasingly used in maize breeding trials, there is a reasonable need for software tools that can automatically identify visual phenotypic features of maize plants and implement batch processing on image datasets.ResultsOn the boundary between computer vision and plant science, we utilize advanced deep learning methods based on convolutional neural networks to empower the workflow of maize phenotyping analysis. This paper presents Maize-IAS (Maize Image Analysis Software), an integrated application supporting one-click analysis of maize phenotype, embedding multiple functions: (I) Projection, (II) Color Analysis, (III) Internode length, (IV) Height, (V) Stem Diameter and (VI) Leaves Counting. Taking the RGB image of maize as input, the software provides a user-friendly graphical interaction interface and rapid calculation of multiple important phenotypic characteristics, including leaf sheath points detection and leaves segmentation. In function Leaves Counting, the mean and standard deviation of difference between prediction and ground truth are 1.60 and 1.625.ConclusionThe Maize-IAS is easy-to-use and demands neither professional knowledge of computer vision nor deep learning. All functions for batch processing are incorporated, enabling automated and labor-reduced tasks of recording, measurement and quantitative analysis of maize growth traits on a large dataset. We prove the efficiency and potential capability of our techniques and software to image-based plant research, which also demonstrates the feasibility and capability of AI technology implemented in agriculture and plant science.

Dataset Information

Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software.

Unlabelled

Availability and implementation

Contact

Supplementary information

Publications

Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software.

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