BAFFLE: A 3D Printable Device for Macroscopic Quantification of Fluorescent Bacteria in Space and Time

Abstract

Despite the ubiquity and importance of microbial communities, understanding the population dynamics of mixed cultures in structured environments remains a fundamental problem in microbial ecology. Identifying bacterial strains within a complex microbial community represents a challenging technical problem. We describe a low-cost optomechanical device designed to acquire multi-channel timelapse images of bacterial colonies growing in agar plates. This device uses a system of addressable LEDs and fluorescence filters to estimate the spatio-temporal distribution of different fluorescently-tagged cells from time-lapse images obtained using a standard DSLR camera with a macro lens. We demonstrate the potential of this device with a range of applications from experimental microbiology.

NIRis: A low-cost, versatile imaging system for near-infrared fluorescence detection of phototrophic cell colonies used in research and education

“…However, the use of a hyperspectral camera places it in a different price category. Likewise more sophisticated is an open-source fluorescence imaging device which utilizes filter cubes, an incubation chamber and a consumer-grade DSLR camera with macro lens [ 25 ] Besides the higher costs, this set-up is restricted to the detection of signals in the visible light range, unless the internal hot mirror of the camera is removed.…”

Fabrication and validation of an LED array microscope for multimodal, quantitative imaging

“…Open hardware microscope designs tend to be purpose built for specific imaging modalities, including but not limited to fluorescence [30] , brightfield [17] , [31] , darkfield, and light sheet imaging [32] . Although this specificity in design lowers the overall cost and complexity, it limits the application of these systems to different modalities or use cases.…”

“…This XY-stage has remarkable speed, precision and accuracy, as required for some cases, such as drug screening [8] . However, there are multiple open hardware designs that can deliver accuracy in the micrometer range for a significantly reduced price [16] , [17] , [18] , [30] , [33] . Most of these open-source designs are made for biological applications and allow for smaller scale experiments to be performed.…”

NIRis: A low-cost, versatile imaging system for NIR fluorescence detection of phototrophic cell colonies used in science and education

“…However, the use of a hyperspectral camera places it in a different price category. Likewise more sophisticated is an open-source fluorescence imaging device which utilizes filter cubes, an incubation chamber and a consumer-grade digital single-lens reflex (DSLR) camera with macro lens [19] Besides the higher costs, this set-up is restricted to the detection of signals in the visible light range, unless the internal hot mirror of the camera is removed.…”