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Supporting the Open-Source CellProfiler Codebase

Award Imaging Software Fellow


Allen Goodman

Broad Institute of MIT and Harvard


Allen Goodman, a Senior Software Engineer at the Broad Institute of MIT and Harvard, working in the lab of Anne Carpenter, will support the existing open-source CellProfiler codebase as part of contributing to collaborative, open-source projects that will benefit the entire bioimaging software ecosystem. Goodman will focus on the most important collaborative projects needed to transition the bioimaging software ecosystem towards the use of deep learning and web-based applications. This will include a web application for evaluating segmentation algorithms that help analyze images, training a deep learning model to robustly detect nuclei across experimental setups, and creating a deep learning-based tool to classify cell types. Goodman will also assess and improve integration between CellProfiler and other key bioimaging software libraries, such as scikit-image.

Project Description

The open-source CellProfiler has been used in a wide range of experiments, analyzing images of specimens such as cells, yeast colonies, and worms in support of research on diseases ranging from breast cancer and leukemia, to liver disease and HIV. The software has been cited over 6,200 times since being published in October 2006.