Embedded Files
Mouse Container
The mouse tank serves as the primary imaging enclosure for the ultrasound platform and is designed to safely house the mouse during in vivo scanning procedures. The tank allows the mouse's body to remain submerged in a water bath while keeping the head above the water surface for anesthetic delivery and continuous monitoring. Water is used as the acoustic coupling medium because it efficiently transmits ultrasound waves between the probe and the subject, enabling high-quality image acquisition. The enclosure incorporates a neck sealing mechanism to minimize water leakage while maintaining animal safety and comfort during insertion and imaging. By providing a controlled and repeatable imaging environment, the mouse tank improves experimental consistency and serves as the foundation for accurate 3D ultrasound data collection and volumetric reconstruction.
Positioning Stage
The positioning stage is responsible for supporting and precisely controlling the movement of the Clarius ultrasound probe during imaging procedures. The system utilizes motorized linear actuators to translate the probe along the X-axis, parallel to the length of the mouse, and the Z-axis, perpendicular to the imaging surface. This controlled motion enables the probe to acquire a series of ultrasound images at known spatial intervals, which is essential for accurate 3D volumetric reconstruction. By automating probe movement, the positioning stage reduces operator variability, improves scan repeatability, and allows researchers to collect consistent imaging data more efficiently than with manual positioning methods. The stage is designed to provide stable, low-vibration motion while supporting the weight of the probe and associated mounting hardware throughout the scanning process.
Electronics/Controls
The electronics enclosure serves as the control center of the imaging platform, housing the components required to power, monitor, and operate the system. A 24 V power supply provides electrical power to the motion control hardware, while dedicated stepper motor drivers control the X-axis and Z-axis actuators responsible for probe positioning. A waterproof temperature sensor is integrated into the system to monitor water temperature within the mouse tank, helping researchers maintain appropriate imaging conditions throughout an experiment. System coordination and motor control are managed by a Raspberry Pi Pico microcontroller mounted on a soldered prototyping board, which provides a compact and reliable platform for integrating sensor inputs and motion commands. By consolidating all electrical components into a dedicated enclosure separate from the water-filled imaging environment, the design improves organization, safety, and ease of operation while supporting precise and repeatable ultrasound imaging procedures.
Software and GUI
The software and graphical user interface (GUI) provide researchers with a centralized platform for controlling the imaging system and monitoring experimental conditions in real time. Through the GUI, users can connect to supported ultrasound probes, view a live ultrasound imaging feed, and monitor the current position of the probe alongside real-time water temperature measurements. The interface allows researchers to home the positioning stage, define scan start positions, configure scan parameters, and prevent motion commands that exceed the physical travel limits of the X-axis and Z-axis actuators. Additional features include scan simulation, cine scanning for reduced acquisition times, automated scanning with programmed pauses to minimize vibration-induced image artifacts, a scan progress indicator, estimated scan completion time, and an emergency stop function for enhanced safety. Following image acquisition, an external Python-based reconstruction script can process the collected image and position data to generate three-dimensional volumetric representations of the scanned region. Together, the software and GUI streamline system operation, improve usability, and enable repeatable and efficient ultrasound imaging workflows.
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