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Open for (Cell) Science: Allen Cell and Structure Segmenter

September 21, 2021

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Open for (cell) science

An open source tool for 3D segmentation of intracellular structures in fluorescence microscopy images

The Allen Cell and Structure Segmenter is a Python-based open source toolkit that enables users to combine classic image segmentation with iterative deep learning workflows. We developed a set of 20 classic image segmentation workflows that serve as a “lookup table” reference and starting point for users, and also made this available as a plugin for the Napari viewer. The iterative deep learning workflow can take over when the classic segmentation workflow is insufficient. Two straightforward “human-in-the-loop” curation strategies convert a set of classic image segmentation workflow results into a set of 3D ground truth images for iterative model training without the need for manual painting in 3D. This webinar will prepare you to use the Allen Cell and Structure Segmenter in your research to process 3D fluorescent images for quantitative analysis. Presented by Kimberly R. Metzler, PhD, Senior Scientific Program Manager, and Kaytlyn Gerbin, PhD, Scientist.



September 21
10:00 am - 11:00 am




Allen Institute for Cell Science