Potentially a useful tool…
Functional Ultrasound Imaging from Scratch
Functional ultrasound imaging (fUSI) is just now emerging as a viable path towards high-res mapping of cortex. Unpacking the acronym, functional ultrasound imaging means:
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it’s functional, as opposed to structural — it tracks brain activity, not just anatomy;
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it uses ultrasound, sound at in the MHz range generated by piezoelectric transducers is transmitted through the tissue, and reflections are measured at the surface
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it’s imaging, it produces actual spatial maps.
I’ve read my fair share of material about the promise of fUSI, but I’ve found it lacking in detail. fUSI picks on the hemodynamic response, but how exactly? What’s the source of contrast? Does it measure blood flow or volume? How does reconstruction work exactly? How does it deal with motion of the head? What is ultrasound, anyway?
There’s remarkably little accessible information about the mechanics of fUSI online. That’s because it’s quite a new modality, and most of the knowledge lives scattered across methods sections in papers, often missing context. As a (reformed) physicist, what I find satisfying is to be able to simulate the physical phenomena using code–what I cannot build, I don’t understand, etc. Unfortunately, the best simulation tools for ultrasound have historically been in MATLAB, and I’m not going down that rabbit hole again. Instead, I wrote a series of Python tutorials to lower the barrier to entry into ultrasound. Before I get to those, here’s a quick overview of what fUSI is and how it works; if that makes you curious to learn, have a look at the notebooks on Github.
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