Plant Image Analysis Plant Image Analysis


Broad Institute

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Scientific article
CellProfiler: image analysis software for identifying and quantifying cell phenotypes.
AE. Carpenter, TR. Jones, MR. Lamprecht, C. Clarke, IH. Kang, O. Friman, DA. Guertin, JH. Chang, RA. Lindquist, J. Moffat, P. Golland, DM. Sabatini,
2006 , Genome Biol. , 7(10), 0
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CellProfiler is freely available modular image analysis software that is capable of handling hundreds of thousands of images. The software contains already-developed methods for many cell types and assays and is also an open-source, flexible platform for the sharing, testing, and development of new methods by image analysis experts.

CellProfiler meets the following needs: advanced algorithms for image analysis that are able to accurately identify crowded cells and non-mammalian cell types; a modular, flexible design allowing analysis of new assays and phenotypes; open-source code so the underlying methodology is known and can be modified or improved by others; a user-friendly interface; the capability to make use of clusters of computers when available; and a design that eliminates the tedium of the many steps typically involved in image analysis, many of which are not easily transferable from one project to another (for example, image formatting, combining several image analysis steps, or repeating the analysis with slightly different parameters).

CellProfiler was designed and optimized for the most common high-content screening image format, that is, two-dimensional images.

Source: Carpenter et al. (2006) Genome biology , 7(10)

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Operating system
windows, mac, linux,


Measured variables
shape, localisation, surface,

Automation level

Plant requirements

Image requirements

Export formats
txt, SQL database,

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