Introduction
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. This toolkit brings together classic image segmentation and iterative deep learning workflows first to generate initial high-quality 3D intracellular structure segmentations and then to easily curate these results to generate the ground truths for building robust and accurate deep learning models. The toolkit takes advantage of the high replicate 3D live cell image data collected at the Allen Institute for Cell Science of over 30 endogenous fluorescently tagged human induced pluripotent stem cell (hiPSC) lines. Each cell line represents a different intracellular structure with one or more distinct localization patterns within undifferentiated hiPS cells and hiPSC-derived cardiomyocytes.
Overview
The Allen Cell Structure Segmenter consists of two complementary elements, a classic image segmentation workflow, with a restricted set of algorithms and parameters, and an iterative deep learning segmentation workflow. We created a collection of 20 classic image segmentation workflows based on 20 distinct and representative intracellular structure localization patterns as a “lookup table” reference and starting point for users. 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. The Allen Cell Structure Segmenter thus leverages state of the art computer vision algorithms in an accessible way to facilitate their application by the experimental biology researcher.
To access the toolkit, please check out our Github repository and the accompanying paper on bioRxiv. Currently, only the classic image segmentation workflow is included in our Github repository. We are working on the software engineering side of the iterative deep learning workflow to make it openly available in early 2019.
To access the toolkit, please check out our Github repository and the accompanying paper on bioRxiv. Currently, only the classic image segmentation workflow is included in our Github repository. We are working on the software engineering side of the iterative deep learning workflow to make it openly available in early 2019.
Video tutorial
Stay tuned for a video tutorial - coming in June - to walk you step-by-step in using the Allen Cell Structure Segmenter. The tutorial will include sample data.
Lookup table of classic image segmentation worksflows for 20 intracellular structure localization patterns
Click on thumbnail to view video
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Full z-stack examples
*Note: all scale bars in these movies are 10μm
*Note :
- Due to the lag between development and production cycles, the segmentation results on Data Download page are continuously being updated using our new toolkit. In the meantime, applying our code on Github can produce our most recent segmentation results.
- We appreciate your feedback. Please sign-up on our Allen Cell Discussion Forum for community questions and comments.