A feedback-driven IoT microfluidic, electrophysiology, and imaging platform for brain organoid studies.

The analysis of tissue cultures, particularly brain organoids, takes a high degree of coordination, measurement, and monitoring. We have developed an automated research platform enabling independent devices to achieve collaborative objectives for feedback-driven cell culture studies. Unified by an Internet of Things (IoT) architecture, our approach enables continuous, communicative interactions among various sensing and actuation devices, achieving precisely timed control of in vitro biological experiments. The framework integrates microfluidics, electrophysiology, and imaging devices to maintain cerebral cortex organoids and monitor their neuronal activity. The organoids are cultured in custom, 3D-printed chambers attached to commercial microelectrode arrays for electrophysiology monitoring. Periodic feeding is achieved using programmable microfluidic pumps. We developed computer vision fluid volume estimations of aspirated media, achieving high accuracy, and used feedback to rectify deviations in microfluidic perfusion during media feeding/aspiration cycles. We validated the system with a 7-day study of mouse cerebral cortex organoids, comparing manual and automated protocols. The automated experimental samples maintained robust neural activity throughout the experiment, comparable with the control samples. The automated system enabled hourly electrophysiology recordings that revealed dramatic temporal changes in neuron firing rates not observed in once-a-day recordings.

Modular automated microfluidic cell culture platform reduces glycolytic stress in cerebral cortex organoids.

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.

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.

Picroscope: low-cost system for simultaneous longitudinal biological imaging.

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.

Real-Time Sensing with Patterned Plasmonic Substrates and a Compact Imager Chip.

Optical sensing is an important research field due to its proven ability to be extremely sensitive, nondestructive, and applicable to sensing a wide range of chemical, thermal, electric, or magnetic phenomena. Beyond traditional optical sensors that often rely on bulky setups, plasmonic nanostructures can offer many advantages based on their sensitivity, compact form, cost-effectiveness, multiplexing compatibility, and compatibility with many standard semiconductor nanofabrication techniques. In particular, plasmon-enhanced optical transmission through arrays of nanostructured holes has led to the development of a new generation of optical sensors. In this chapter we present a simple fabrication technique to use plasmonic nanostructures as compact sensors. We position the nanohole array, an LED illumination source, and a spacer layer directly on top of a standard complementary metal-oxide-semiconductor (CMOS) imager chip. This setup is a viable sensor platform in both liquid and gas environments. These devices could operate as low-cost sensors for environmental monitoring, security, food safety, or monitoring small-molecule binding to extract affinity information and binding constants.

Direct spectral imaging of plasmonic nanohole arrays for real-time sensing.

Plasmon-enhanced optical transmission through arrays of nano-structured holes has led to the development of a new generation of optical sensors. In this paper, to dramatically simplify the standard optical setups of these sensors, we position the nanoholes, an LED illumination source and a spacer layer directly on top of a CMOS imager chip. Transmitted light diffracts from the nanohole array, spreading into a spectrum over the space of a millimeter to land on the imager as a full spectrum. Our chip is used as a sensor in both a liquid and a gas environment. The spectrum is monitored in real-time and the plasmon-enhanced transmission peaks shift upon exposure to different concentrations of glycerol-in-water solutions or ethanol vapors in nitrogen. While liquids provide good refractive index contrast for sensing, to enhance sensitivity to solvent vapors, we filled the nanoholes with solvatochromic dyes. This on-chip solution circumvents the bulky components (e.g. microscopes, coupling optics, and spectrometers) needed for traditional plasmonic sensing setups, uses the nanohole array as both the sensing surface and a diffraction grating, and maintains good sensitivity. Finally, we show simultaneous sensing from two side-by-side locations, demonstrating potential for multiplexing and lab on a chip integration.