​The Allen Cell Structure Segmenter

​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. Classic image segmentation workflows for 20 distinct intracellular structure localization patterns. A visual “lookup table” is outlining the modular algorithmic steps for each segmentation workflow. This provides an intuitive guide for selection or construction of new segmentation workflows for a user’s particular segmentation task. 
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. Importantly, this module was not released yet.