Low cost cloud based remote microscopy for biological sciences

Baudin, Pierre V.; Ly, Victoria T.; Pansodtee, Pattawong; Jung, Erik; Currie, R.; Hoffman, Ryan N.; Willsey, Helen Rankin; Pollen, Alex A.; Nowakowski, Tomasz J.; Haussler, David; Mostajo-Radji, Mohammed A.; Salama, Sofie R.; Teodorescu, Mircea

doi:10.1016/j.iot.2021.100454

Cited by 15 publications

(18 citation statements)

References 27 publications

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“…A computer vision algorithm was used to detect the features in focus at each focal plane, generate a composite image maximizing the in-focus features in the entire organoid, and compute the projected area. This process is described in previous work 35 . Figure 6B shows 12 cerebral cortex organoid cultures (day 12), loaded in individual wells of the microfluidic chip and fed in parallel on the Autoculture platform for the experiment.…”

Section: Live Imagingmentioning

confidence: 99%

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

Seiler

Mantalas

Selberg

et al. 2022

Preprint

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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.

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Section: Live Imagingmentioning

confidence: 99%

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

Seiler

Mantalas

Selberg

et al. 2022

Preprint

Self Cite

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“…An outline of existing tools that utilize the platform described in this paper. (Assay) shows the Picroscope Ly et al (2021); Baudin et al (2021) for microscopy, the Piphys Voitiuk et al (2021) for electrophysiology recording, and a fully automated auto-culture system for media recording and replacement. (Infrastructure) shows the primary suite of tools introduced in section 2.2, 2.4 and 2.5 in this paper.…”

Section: System Designmentioning

confidence: 99%

“…(Analysis) demos some of the reports produced as a result of the workflows that run as post-processing jobs. (the “Picroscope” and “Piphys” figures are adapted from Ly et al (2021); Baudin et al (2021) and Voitiuk et al (2021))…”

Section: System Designmentioning

confidence: 99%

Internet of Things Architecture for Cellular Biology

Parks

Voitiuk

Geng

et al. 2021

Preprint

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New cell culture techniques have led to complex tissue models in biological experiments. For example, 3-D cerebral organoids provide a more realistic model of the human cortical tissue. However, these cell culture experiments are restricted by high costs and limited labor. A massively scalable and cost efficient platform for tissue experiments would benefit genomics, neuroscience, and translational medicine by enabling advanced high throughput tissue screens. Cloud computing and the Internet of Things (IoT) provide new tools for managing multiple experiments in parallel that are remotely controlled through automation. We introduce a cloud-based IoT architecture that takes advantage of these tools to offer an environment where researchers can run thousands of cell culture experiments at once. This technology allows studies with cell cultures to be performed at scales far beyond a single lab setting, democratizing access to advanced tissue models and enabling new avenues of research.

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“…Unlike systems that involve direct physical interaction with samples, remote imaging systems are non-invasive and capable of being set up at a low cost. Imaging systems capable of performing near real-time simultaneous longitudinal tracking of cells, 3D cultures, and small organisms have started to emerge in research settings [36, 37, 38]. These systems can be used to perform experiments with a diversity of models and conditions.…”

Section: Introductionmentioning

confidence: 99%

“…These systems can be used to perform experiments with a diversity of models and conditions. The rapid cloud-based transfer and storage of data and their relatively simple interfaces make them excellent tools for science [37, 38]. Given the versatility of these devices, applying them to remote education represents a cost-effective and scalable approach to performing PBL.…”

Section: Introductionmentioning

confidence: 99%

Cloud-controlled microscopy enables remote project-based biology education in Latinx communities in the United States and Latin America

Baudin

Sacksteder

Worthington

et al. 2022

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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 allowing simultaneous interaction by many students worldwide. 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 repeat standard classroom experiments. To investigate the impact of this program, we designed and ran six user studies with students worldwide. All experiments were executed 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' conclusion, 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.

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Low cost cloud based remote microscopy for biological sciences

Cited by 15 publications

References 27 publications

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

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

Internet of Things Architecture for Cellular Biology

Cloud-controlled microscopy enables remote project-based biology education in Latinx communities in the United States and Latin America

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