A Reconfigurable Real-Time Compressive-Sampling Camera for Biological Applications

Abstract

Many applications in biology, such as long-term functional imaging of neural and cardiac systems, require continuous high-speed imaging. This is typically not possible, however, using commercially available systems. The frame rate and the recording time of high-speed cameras are limited by the digitization rate and the capacity of on-camera memory. Further restrictions are often imposed by the limited bandwidth of the data link to the host computer. Even if the system bandwidth is not a limiting factor, continuous high-speed acquisition results in very large volumes of data that are difficult to handle, particularly when real-time analysis is required. In response to this issue many cameras allow a predetermined, rectangular region of interest (ROI) to be sampled, however this approach lacks flexibility and is blind to the image region outside of the ROI. We have addressed this problem by building a camera system using a randomly-addressable CMOS sensor. The camera has a low bandwidth, but is able to capture continuous high-speed images of an arbitrarily defined ROI, using most of the available bandwidth, while simultaneously acquiring low-speed, full frame images using the remaining bandwidth. In addition, the camera is able to use the full-frame information to recalculate the positions of targets and update the high-speed ROIs without interrupting acquisition. In this way the camera is capable of imaging moving targets at high-speed while simultaneously imaging the whole frame at a lower speed. We have used this camera system to monitor the heartbeat and blood cell flow of a water flea (Daphnia) at frame rates in excess of 1500 fps.

Development of a low-cost, user-customizable, high-speed camera

“…It was also found to be well suited for high resolution forward-scattering and in-line imaging like bright-field microscopy, which similarly makes biology and microscopy a key application area for our camera as well. The field of microscopy has seen research in similar spirit to ours with a low-cost, open-source multi-fluorescence imaging system [21], and our solution can help accelerate or remove unneeded complexity in high-speed designs, such as in [22] which required a custom-built sensor, DAQ card, and host computer for the high-speed imaging of the blood flow and heartbeat of live Daphnia.…”

Open Source Software to Control Bioflo Bioreactors

“…A QSM can be accompanied with a producer-consumer pattern (QSM-PC) to decouple asynchronous processes. Examples of QSM-PC implementation are the decoupling of data acquisition from data analysis [15] , hardware control from hardware communication [16] , and user interactions from code execution [13] .…”