OCTOPUS: A versatile open-source tool creating realistic numericalbrain cells
Brain cell morphology plays a crucial role in function and pathology. Biophysical models of diffusion MRI (dMRI) quantify cell morphology in vivo, enabling the design of novel biomarkers. These models represent cells by simplified geometries, such as spheres and randomly oriented cylinders, for which analytical signal expressions exist. However, dMRI signals are sensitive to morphological…
The OCTOPUS toolbox, an open-source tool, has been developed to create digital replicas of brain cells with a wide range of geometrical features. Brain cell morphology plays a significant role in both function and pathology, and biophysical models of diffusion MRI (dMRI) are used to quantify cell morphology in vivo. These models often simplify cell geometries, such as spheres and cylinders, but fail to account for complex features like branching, tapering, and protrusions.
The OCTOPUS toolbox, available through the Python interface OCTOpool, generates cells with all these intricate geometrical features. The researchers used OCTOPUS to recreate histologically reconstructed neuronal and glial cells, including pyramidal, GABAergic, and glutamatergic neurons, as well as astro- and microglia. By comparing the geometries and dMRI signals of generated and original cells, the researchers found that different growth strategies are suitable for more isotropic and anisotropic cells.
This tool has the potential to validate biophysical models, design dMRI sequences sensitive to fine-grained cell morphology, and generate realistic numerical substrates of brain tissue.
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