​The Allen Cell Structure Segmenter

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
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2-clause BSD license plus clause a third clause that prohibits redistribution for commercial purposes without further permission.

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.


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