For a transparent well with a known volume capacity, changes in fluid level result in predictable changes in magnification of an overhead light source. For a given well size and fluid, the relationship between volume and magnification can be calculated if the fluid’s index of refraction is known or in a naive fashion with a calibration procedure. Light source magnification can be measured through a camera and processed using computer vision contour analysis with OpenCV. This principle was applied in the design of a 3D printable sensing device using a raspberry pi zero and a camera
Organ-on-a-chip systems combine microfluidics, cell biology, and tissue engineering to culture 3D organ-specific in vitro models that recapitulate the biology and physiology of their in vivo counterparts. Here, we have developed a multiplex platform that automates the culture of individual organoids in isolated microenvironments at user-defined media flow rates. Programmable workflows allow the use of multiple reagent reservoirs that may be applied to direct differentiation, study temporal variables, and grow cultures long term. Novel techniques in polydimethylsiloxane (PDMS) chip fabrication are described here that enable features on the upper and lower planes of a single PDMS substrate. RNA sequencing (RNA-seq) analysis of automated cerebral cortex organoid cultures shows benefits in reducing glycolytic and endoplasmic reticulum stress compared to conventional in vitro cell cultures.
IoT cloud laboratory: Internet of Things architecture for cellular biology
David F. Parks, Kateryna Voitiuk, Jinghui Geng, and
20 more authors
The Internet of Things (IoT) provides a simple framework to control online devices easily. IoT is now a commonplace tool used by technology companies but is rarely used in biology experiments. IoT can benefit cloud biology research through alarm notifications, automation, and the real-time monitoring of experiments. We developed an IoT architecture to control biological devices and implemented it in lab experiments. Lab devices for electrophysiology, microscopy, and microfluidics were created from the ground up to be part of a unified IoT architecture. The system allows each device to be monitored and controlled from an online web tool. We present our IoT architecture so other labs can replicate it for their own experiments.
Project-based learning (PBL) has long been recognized as an effective way to teach complex biology concepts. However, not all institutions have the resources to facilitate effective project-based coursework for students. We have developed a framework for facilitating PBL using remote-controlled internet-connected microscopes. Through this approach, one lab facility can host an experiment for many students around the world simultaneously. Experiments on this platform can be run on long timescales and with materials that are typically unavailable to high school classrooms. This allows students to perform novel research projects rather than just repeating standard classroom experiments. To investigate the impact of this program, we designed and ran six user studies with students worldwide. All experiments were hosted in Santa Cruz and San Francisco, California, with observations and decisions made remotely by the students using their personal computers and cellphones. In surveys gathered after the experiments, students reported increased excitement for science and a greater desire to pursue a career in STEM. This framework represents a novel, scalable, and effective PBL approach that has the potential to democratize biology and STEM education around the world.
2021
Low cost cloud based remote microscopy for biological sciences
Pierre V. Baudin, Victoria T. Ly, Pattawong Pansodtee, and
10 more authors
A low cost remote imaging platform for biological applications was developed. The “Picroscope” is a device that allows the user to perform longitudinal imaging studies on multi-well cell culture plates. Here we present the network architecture and software used to facilitate communication between modules within the device as well as system communication with external cloud services. A web based console was created to control the device and view experiment results. Post processing tools were developed to analyze captured data in the cloud. The result is a platform for monitoring biological experiments from outside the lab.
Picroscope: low-cost system for simultaneous longitudinal biological imaging
Victoria T. Ly, Pierre V. Baudin, Pattawong Pansodtee, and
16 more authors
Simultaneous longitudinal imaging across multiple conditions and replicates has been crucial for scientific studies aiming to understand biological processes and disease. Yet, imaging systems capable of accomplishing these tasks are economically unattainable for most academic and teaching laboratories around the world. Here, we propose the Picroscope, which is the first low-cost system for simultaneous longitudinal biological imaging made primarily using off-the-shelf and 3D-printed materials. The Picroscope is compatible with standard 24-well cell culture plates and captures 3D z-stack image data. The Picroscope can be controlled remotely, allowing for automatic imaging with minimal intervention from the investigator. Here, we use this system in a range of applications. We gathered longitudinal whole organism image data for frogs, zebrafish, and planaria worms. We also gathered image data inside an incubator to observe 2D monolayers and 3D mammalian tissue culture models. Using this tool, we can measure the behavior of entire organisms or individual cells over long-time periods.
