Jianxu Chen https://orcid.org/0000-0002-8500-1357
Liya Ding
Matheus P. Viana https://orcid.org/0000-0001-9288-2108
Melissa C. Hendershott
Ruian Yang
Irina A. Mueller
Susanne M. Rafelski

The Allen Cell Structure Segmenter is a Python-based open source toolkit developed at the Allen Institute for Cell Science for 3D segmentation of intracellular structures in fluorescence microscope images.

It consists of two complementary elements: (1) image segmentation workflows for 20 distinct intracellular structure localization patterns. (2) Human-in-the-loop iterative deep learning segmentation workflow trained on ground truth manually curated data from the images segmented with the segmentation workflow.