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CellWalker: a user-friendly and modular computationalpipeline for morphological analysis of microscopy images

Bioimage informatics

Harshavardhan Khare*, Nathaly Dongo Mendoza*, Chiara Zurzolo


The implementation of computational tools for analysis of microscopy images has been one of the most important technological

innovations in biology, providing researchers unmatched capabilities to comprehend cell shape and connectivity. While numerous tools exist for

image annotation and segmentation, there is a noticeable gap when it comes to morphometric analysis of microscopy images. Most existing

tools often measure features solely on 2D serial images, which can be difficult to extrapolate to 3D. For this reason, we introduce CellWalker, a

computational toolbox that runs inside Blender, an open-source computer graphics software. This add-on improves the morphological analysis

by seamlessly integrating analysis tools into the Blender workflow, providing visual feedback through a powerful 3D visualization, and leveraging

the resources of Blender’s community. CellWalker provides several morphometric analysis tools that can be used to calculate distances, volume,

surface areas and to determine cross-sectional properties. It also includes tools to build skeletons, calculate distributions of subcellular organelles.

In addition, this python-based tool contains ‘visible-source’ IPython notebooks accessories for segmentation of 2D/3D microscopy images

using deep learning and visualization of the segmented images that are required as input to CellWalker. Overall, CellWalker provides practical

tools for segmentation and morphological analysis of microscopy images in the form of an open-source and modular pipeline which allows a

complete access to fine-tuning of algorithms through visible-source code while still retaining a result-oriented interface.

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