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Review: Biological Imaging Software Tools



Anne L. Plant, Kevin Eliceiri, Anne Carpenter


Few technologies are more widespread in modern biological laboratories than imaging by microscopy. Advancements in optical technologies and instrumentation over the past twenty years have led to massive improvements in the resolution, specificity, dimensionality, complexity, and scale of imaging experiments. Almost all such advancements have required the development of accompanying imaging software to enable the acquisition, management, analysis, and visualization of the imaging data. In this article, we review each computational step that biologists encounter when dealing with digital images from light microscopy and the challenges in that domain. We also describe the overall status of available software for each stage of the bioimaging informatics workflow as well as systems covering the entire workflow, with an emphasis on open-source options.
Nature Methods


imaging, biology, microscopy, software, computational, open-source


Plant, A. , Eliceiri, K. and Carpenter, A. (2012), Review: Biological Imaging Software Tools, Nature Methods, [online], (Accessed May 28, 2024)


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Created August 29, 2012, Updated February 19, 2017