Biology subjects

Kjer, H. M.

Publications and source records attributed to Kjer, H. M..

3 recordsLinked to original sources

bioRxiv2021

Does powder averaging remove dispersion bias in diffusion MRI diameter estimates within real 3D axonal architectures?

Noninvasive estimation of axon diameter with diffusion MRI holds potential to investigate the dynamic properties of the brain network and pathology of neurodegenerative diseases. Recent methods use powder averaging to account for complex white matter architectures, such as fibre crossing regions, but these have not been validated for real axonal geometries. Here, we present 120 - 313 m long segmented axons from X-ray nano-holotomography volumes of a splenium and crossing fibre region of a vervet monkey brain. We show that the axons in the complex crossing fibre region, which contains callosal, association, and corticospinal connections, are larger and exhibit a wider distribution than those of the splenium region. To accurately estimate the axon diameter in these regions, therefore, sensitivity to a wide range of diameters is required. We demonstrate how the q-value, b-value, signal-to-noise ratio and the assumed intra-axonal parallel diffusivity influence the range of measurable diameters with powder average approaches. Furthermore, we show how Gaussian distributed noise results in a wider range of measurable diameter at high b-values than Rician distributed noise, even at high signal-to-noise ratios of 100. The number of gradient directions is also shown to impose a lower bound on measurable diameter. Our results indicate that axon diameter estimation can be performed with only few b-shells, and that additional shells do not improve the accuracy of the estimate. Through Monte Carlo simulations of diffusion, we show that powder averaging techniques succeed in providing accurate estimates of axon diameter across a range of sequence parameters and diffusion times, even in complex white matter architectures. At sufficiently low b-values, the acquisition becomes sensitive to axonal microdispersion and the intra-axonal parallel diffusivity shows time dependency at both in vivo and ex vivo intrinsic diffusivities.

neuroscience↗

bioRxiv2020

InSegtCone: Interactive Segmentation of crystalline Cones in compound eyes

Understanding the diversity of eyes is crucial to unravel how different animals use vision to interact with their respective environments. To date, comparative studies of eye anatomy are scarce because they often involve time-consuming or inefficient methods. X-ray micro-tomography is a promising high-throughput imaging technique that enables to reconstruct the 3D anatomy of eyes, but powerful tools are needed to perform fast conversions of anatomical reconstructions into functional eye models. We developed a computing method named InSegtCone to automatically segment the crystalline cones in the apposition compound eyes of arthropods. Here, we describe the full auto-segmentation process, showcase its application to three different insect compound eyes and evaluate its performance. The auto-segmentation could successfully label the full individual shapes of 60%-80% of the crystalline cones, and is about as accurate and 250 times faster than manual labelling of the individual cones. We believe that InSegtCone can be an important tool for peer scientists to enable extensive comparisons of the diversity of eyes and vision in arthropods.

zoology↗

bioRxiv2020

Axon morphology is modulated by the local environment and impacts the non-invasive investigation of its structure-function relationship

Axonal conduction velocity, which ensures efficient function of the brain network, is related to axon diameter. Non-invasive, in vivo axon diameter estimates can be made with diffusion magnetic resonance imaging, but the technique requires 3D validation. Here, high resolution, 3D synchrotron X-ray Nano-Holotomography images of white matter samples from the corpus callosum of a monkey brain reveal that blood vessels, cells and vacuoles affect axonal diameter and trajectory. Within single axons, we find that the variance in diameter and conduction velocity correlates with the mean diameter, contesting the value of precise diameter determination in larger axons. These complex 3D axon morphologies drive previously reported 2D trends in axon diameter and g-ratio. Furthermore, we find that these morphologies bias the estimates of axon diameter with diffusion magnetic resonance imaging and, ultimately, impact the investigation and formulation of the axon structure-function relationship.

neuroscience↗