🚨Exciting update🚨
We’ve recently expanded this method to whole-brain single-voxel clustering. Stay tuned for more breakthroughs as we push the limits of high-quality and high-resolution brain imaging with fUS! 🚀🧠✨
The PyfUS software used and described in the paper is available online at https://github.com/OpenfUS/PyfUS
Congratulations to Dr Théo Lambert and all the Urban Lab team 🤩 @fUSI
@_NERF
@KULeuvenOpenScience
GitHub - OpenfUS/PyfUS
Contribute to OpenfUS/PyfUS development by creating an account on GitHub.
Single-voxel clustering expands the fUS signal analysis toolbox! It enables paradigm-free analysis in behaving subjects, atlas-free investigations, and even brain decoding—unlocking new possibilities in neuroimaging 🧠💡
Our work explores the strengths and limitations of each method, offering insights into the trade-offs between dimensionality and comprehensiveness. A must-read for anyone working with fUS signal analysis! 📊🔍
We compared single-voxel clustering with conventional region-averaging and correlation maps to assess their accuracy in capturing contrast modulation effects on hemodynamic responses. How does our approach stack up? Keep reading! 👇
🚀New from Urban Lab in
#eNeuro We used spatiotemporal clustering of single fUS voxels to map visual activity in awake mice. This high-resolution method precisely separates signals, revealing fine-grained activity patterns like never before🧠✨
https://doi.org/10.1523/ENEURO.0438-24.2025
Spatiotemporal Clustering of Functional Ultrasound Signals at the Single-Voxel Level
Functional ultrasound (fUS) imaging is a well-established neuroimaging technology that offers high spatiotemporal resolution and a large field of view. Typical strategies for analysing fUS data comprise either region-based averaging, typically based on reference atlases, or correlation with experimental events. Nevertheless, these methodologies possess several inherent limitations, including a restricted utilisation of the spatial dimension and a pronounced bias influenced by preconceived notions about the recorded activity. In this study, we put forth single-voxel clustering as a third method to address these issues. A comparison was conducted between the three strategies on a typical dataset comprising visually evoked activity in the superior colliculus in awake mice. The application of single-voxel clustering yielded the generation of detailed activity maps, which revealed a consistent layout of activity and a clear separation between haemodynamic responses. This method is best considered as a complement to region-based averaging and correlation. It has direct applicability to challenging contexts, such as paradigm-free analysis on behaving subjects and brain decoding.
Significance Statement The application of spatiotemporal clustering at single-voxel resolution for functional ultrasound (fUS) signal analysis significantly enhances sensitivity in comparison to conventional methods, such as region-based averaging or event correlation. Conventional approaches frequently rely on predefined atlases or specific experimental conditions, which inherently restrict spatiotemporal resolution. In contrast, single-voxel clustering optimises the potential of fUS, facilitating the detection of intricate activity patterns throughout the brain without the necessity for prior assumptions. This approach enables more precise differentiation of hemodynamic responses and more reliable activity mapping. It is particularly advantageous in complex or paradigm-free studies, offering a high-resolution alternative to standard techniques.
🥳🤩Last piece of work from Urban lab
@_NERFin collab with Babin lab from Department of Telecommunications and Information Processing of Gent Uni 🇧🇪
https://doi.org/10.1007/s12021-024-09706-1
Large Scale in vivo Acquisition, Segmentation and 3D Reconstruction of Cortical Vasculature using $$\mu $$ μ Doppler Ultrasound Imaging - Neuroinformatics
The brain is composed of a dense and ramified vascular network of arteries, veins and capillaries of various sizes. One way to assess the risk of cerebrovascular pathologies is to use computational models to predict the physiological effects of reduced blood supply and correlate these responses with observations of brain damage. Therefore, it is crucial to establish a detailed 3D organization of the brain vasculature, which could be used to develop more accurate in silico models. To this end, we have adapted our functional ultrasound imaging platform, previously designed for recording large scale activity, to enable rapid and reproducible acquisition, segmentation and reconstruction of the cortical vasculature. For the first time, it allows us to digitize the cortical $$\sim 100$$ ∼ 100 - $$\mu $$ μ m3 spatial resolution. Unlike most available strategies, our approach can be performed in vivo within minutes. Moreover, it is easy to implement since it requires neither exogenous contrast agents nor long post-processing time. Therefore, we performed a cortex-wide reconstruction of the vasculature and its quantitative analysis, including i) classification of descending arteries versus ascending veins in more than 1500 vessels/animal and ii) rapid estimation of their length. Importantly, we confirmed the relevance of our approach in a model of cortical stroke, which allows rapid visualization of the ischemic lesion. This development contributes to extending the capabilities of ultrasound neuroimaging to better understand cerebrovascular pathologies such as stroke, vascular cognitive impairment and brain tumors, and is highly scalable for the clinic.
Our latest work leaded by Théo Lambert @_NERF for which we have used simultaneous functional ultrasound imaging and Neuropixels recording in 3 regions of the visual pathway to understand how hemodynamics accurately report the diversity of neural signals in space and time.
Here is the papier 👇🏼
https://biorxiv.org/cgi/content/short/2024.07.10.602912v1
🤩Super excited🥳
🚨🚨Functional ultrasound imaging turns OPEN #opensource
The #OpenfUS initiative by Urban lab @_NERF aims to share Hardware, Software, Analytics & Protocols
More transparency, collaboration & accessibility
🗣️Opening talk by Alan Urban in 1 week at the KU Leuven Kulak Ambassador Chair @KULeuvenOpenScience
https://kulak.kuleuven.be/nl/over_kulak/faculteiten/wetenschappen/ambassadors-chair/Symposium-tanter
Our last work on functional ultrasound imaging of #stroke in awake rats has been published in @eLife
@_NERF
https://doi.org/10.7554/eLife.88919.3
Functional ultrasound imaging of stroke in awake rats
Functional ultrasound imaging was used to monitor brain hemodynamics and sensory-evoked thalamocortical functions in awake rats pre- and post-stroke, advancing our understanding toward new therapeutic developments.
