An organelle-agnostic image analysis tool

Access through your institution Buy or subscribe While state-of-the-art microscopy analysis tools are quickly improving our capability to visualize and understand intracellular dynamics,

they still suffer from many limitations. For instance, existing tools are often specialized to specific organelles, limited to electron microscopy organelle data or unable to handle

three-dimensional models. In addition, deep learning methods often produce ‘black box’ predictions that can be difficult for scientists to interpret. In a recent work, Austin E. Y. T.

Lefebvre and colleagues introduce Nellie (short for organellometer), an automated pipeline that is capable of multiscale and comprehensive organelle-agnostic analysis. Nellie provides

spatial and temporal image analysis by extracting and enhancing structural features. Using a modified Frangi filter, Nellie enhances the structural contrast of organelles and allows for

local structure-based segmentation. The filter itself is optimized for and can adapt to handle structures across the spectrum of typical organelle sizes. Organelles are divided into smaller

subcomponents (branches, nodes, and voxels) using hierarchical segmentation, allowing for feature extraction across different resolutions. These hierarchical subcomponents are then used to

produce motion-capture markers that can provide tracking abilities to measure movement across multiple frames. An additional feature of Nellie that is worth highlighting is its design

focused on ease of use and computational accessibility: the method itself is packaged in a Napari plugin that uses graphical user interface point-and-click functionality. This is a preview

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Team https://www.nature.com/natcomputsci/research-cross-journal-editorial-team Michelle Badri Authors * Michelle Badri View author publications You can also search for this author inPubMed 

Google Scholar CORRESPONDING AUTHOR Correspondence to Michelle Badri. RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Badri, M. An organelle-agnostic

image analysis tool. _Nat Comput Sci_ 5, 191 (2025). https://doi.org/10.1038/s43588-025-00785-x Download citation * Published: 24 March 2025 * Issue Date: March 2025 * DOI:

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