Functional ultrasound imaging (fUS/fUSi/fUSI, not to be confounded with FUS, usually used for focused ultrasound) is a neuroimaging technique using ultrafast Doppler ultrasound to follow cerebral blood-volume dynamics with high spatial and temporal resolution.
This page gathers useful papers, software and resources created by the fUSi community. I will try to update it over time as new tools and resources become available!
Probably one of the most useful general resource, especially for beginners, is The Hitchhiker’s Guide to fUSI, a community-maintained website. It contains all general and practical information on imaging acquisition, surgery, Power Doppler reconstruction, preprocessing, registration, functional connectivity, software, literature and laboratories working with fUSI.
The same initiative also hosts an fUSI Discord community. I definitely recommend all users to join, it is quite active and is probably the best place to ask practical questions, discuss acquisition/analysis problems, or hear about meetings, interesting papers or tools.
Montaldo, Urban & Macé, 2022 - Functional Ultrasound Neuroimaging
A great general entry point, with a lot of helpful insights into the biological and physical principles behind fUSi, and also covering a broad range of application.
Annual Review of Neuroscience
Deffieux, Demené & Tanter, 2021 - Functional Ultrasound Imaging: A New Imaging Modality for Neuroscience
An overview of the history of fUSi, technical principles, preclinical/clinical applications, and perspectives for the field.
Neuroscience
Deffieux et al., 2018 - Functional ultrasound neuroimaging: a review of the preclinical and clinical state of the art
An earlier review that remains relevant for understanding how the field developed and seeing where fUSi sits among other neuroimaging modalities.
Current Opinion in Neurobiology
Edelman & Macé, 2021 - Functional ultrasound brain imaging: Bridging networks, neurons, and behavior
A review with a systems-neuroscience perspective, with emphasis on whole-brain recordings, behaving animals and circuit manipulation.
Current Opinion in Biomedical Engineering
Martinez de Paz & Macé, 2021 - Functional ultrasound imaging: A useful tool for functional connectomics?
A more focused review on fUSi advantages and potential limitations for studying resting-state and task-related connectivity and brain-wide networks.
NeuroImage
Urban et al., 2017 - Understanding the neurovascular unit at multiple scales
Discusses fUSi together with multiphoton microscopy. Interesting for placing fUSi in the broader context of neurovascular imaging across different spatial scales.
Advanced Drug Delivery Reviews
Bergel & Pouget, 2026 - Combined electrophysiology and functional ultrasound imaging: opportunities, challenges, and future directions
A recent review, particularly relevant for discussing the combination of fUSi with electrophysiology and the neuronal processes that underlie the fUSi signal.
Journal of Physiology
He et al., 2026 - Functional ultrasound imaging in preclinical brain stimulation: from multimodal readouts to closed-loop neuromodulation
A recent review discussing fUSi in the context of brain stimulation techniques.
Frontiers in Neuroscience
Macé et al., 2011 - Functional ultrasound imaging of the brain
The original paper introducing fUSi in vivo. Beyond its historical importance, it is still a useful starting point for understanding the principle.
Nature Methods
Macé et al., 2013 - Functional ultrasound imaging of the brain: theory and basic principles
A technical paper for understanding the principles of plane-wave compounding, ultrafast acquisition and the relationship between Power Doppler and cerebral blood volume.
IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
Demené et al., 2015 - Spatiotemporal clutter filtering of ultrafast ultrasound data highly increases Doppler and fUltrasound sensitivity
A methodological paper presenting the now-standard SVD-based separation of tissue and blood signals. This is worth reading to understand what happens between beamformed ultrasound data and the final Power Doppler images.
IEEE Transactions on Medical Imaging
Brunner et al., 2021 - Whole-brain functional ultrasound imaging in awake head-fixed mice
This important protocol fully describes how to measure brain-wide activity in awake head-fixed mice using fUSi, from setting up the acquisition to chronic cranial window surgery and data analysis. Codes are provided for acquisition and data anlysis, as well as CAD files for headpost and mouse holder.
Nature Protocols
Le Meur-Diebolt et al., 2026 - Robust functional ultrasound imaging in the awake and behaving brain: A systematic framework for motion artifact removal
A very useful recent study if you work with awake rodents. It systematically benchmarks strategies for dealing with motion-related artifacts, including clutter filtering, scrubbing and confound regression, and proposes two optimized preprocessing strategies.
Imaging Neuroscience
ConfUSIus - a Python package and napari plugin developed specifically for fUSi. It provides building blocks for data I/O, IQ-to-Power-Doppler processing, quality control, registration, atlas integration, signal processing and visualization. It is currently in active beta development and frequently updated. Weekly drop-in hours are organized by the developers on the community Discord server (see above).
ConfUSIus
PyfUS - another open-source Python framework dedicated to fUSI analysis, developed as part of the OpenfUS initiative.
PyfUS documentation - GitHub repository
PyIconeus - the official open-source Python library from Iconeus for reading and handling data produced by the Iconeus One system, including scan, transform, ROI and raw IQ formats.
PyIconeus on GitHub
Functional ultrasound from scratch - educational resource of Python notebooks, covering ultrasound propagation and image reconstruction, Power Doppler, SVD clutter filtering and finally analysis of real data.
Functional ultrasound from scratch
Another important initiative is the effort to integrate functional ultrasound into BIDS — the Brain Imaging Data Structure, the standard already widely used for modalities such as MRI, PET and electrophysiology.
The fUSI-BIDS extension, BEP040, is a community-driven proposal. The goal is to define how raw fUSi data and metadata should be organized and described, making datasets easier to share, reuse and process with common tools.
BEP040 — Functional Ultrasound