Recordings: Which Animal Preparation?¶

There are many ways to do fUSI, depending on the type of preparation and the state of the animal during the recordings. Each has its pros and cons, mostly regarding the level of noise and data quality. Arguably the best signal quality and lower level of artefacts will be reached in anesthetized recordings with a craniotomy, however this is also probably the less physiological state.

The main challenge for functional ultrasound imaging of the brain comes from aberrations created by the skull when the acoustic wave goes through it. Fortunately, similarly to what is routinely done in optical imaging, imaging windows can be prepared by removing the skull and replacing it by a materials transparent to ultrasounds (polymethylpentene - PMP or TPX (Sieu et al., 2015)).

Recording transcranially in freely-moving animals would be an ideal setting, however this results in increased artefacts (Tiran et al., 2017, Rabut et al., 2020). Below is a table summarizing the main preparations employed so far in the field:

In practice:

• Under anesthesia:
  • Most Rat studies are performed after thinning of the skull
  • Mice can be imaged transcranially with minimal loss of data
• In awake animals:
  • Rats tend to be imaged through a chronic implant in a freely moving setting (fixation of an awake rat is quite challenging due to the animal size)
  • Mice can be imaged either through the skull (Ferrier et al., 2020) or after chronic implants (Brunner et al., 2021, Nunez-Elizalde et al., 2022)

For bigger animals (ferrets, macaques), image are mainly performed head-fixed through an imaging window after craniotomy (ferrets: Bimbard et al, 2018; Landemard et al, 2021, 2025; macaques: Dizeux et al, 2019; Claron et al, 2022, 2023).