A robotic system for automated genetic manipulation and analysis of<i>Caenorhabditis elegans</i>

Li, Zihao; Fouad, Anthony D; Bowlin, Peter D; Fan, Yun; He, Siming; Chang, Meng-Chuan; Du, Angelica; Teng, Christopher; Kassouni, Alexander; Ji, Hongfei; Raizen, David M.; Fang-Yen, Christopher

doi:10.1101/2022.11.18.517134

Cited by 2 publications

(3 citation statements)

References 65 publications

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“…Each video was sampled by 5 images that are linearly spaced across the 20 s period, with adjacent images separated by 4 sec. Following previously described methods (30), we deployed a mask-regional convolutional neural network (Mask-RCNN) to detect and identify eggs in each image. The Mask-RCNN model was trained, evaluated, and deployed by PyTorch GPU (v2.0.0 + cu1.1.8) on a system equipped with a 13th Intel(R) Core(TM) i7-13700K processor and an NVIDIA GeForce RTX 4080 GPU.…”

Section: Methodsmentioning

confidence: 99%

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Automated multimodal imaging ofCaenorhabditis elegansbehavior in multi-well plates

Ji,

Chen,

Fang-Yen

2024

Preprint

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Assays of behavior in model organisms play an important role in genetic screens, drug testing, and the elucidation of gene-behavior relationships. We have developed an automated, high-throughput imaging and analysis method for assaying behaviors of the nematode C. elegans. We use high-resolution optical imaging to longitudinally record the behaviors of 96 animals at a time in multi-well plates, and computer vision software to quantify the animals' locomotor activity, behavioral states, and egg laying events. To demonstrate the capabilities of our system we used it to examine the role of serotonin in C. elegans behavior. We found that egg-laying events are preceded by a period of reduced locomotion, and that this decline in movement requires serotonin signaling. In addition, we identified novel roles of serotonin receptors SER-1 and SER-7 in regulating the effects of serotonin on egg laying across roaming, dwelling, and quiescent locomotor states. Our system will be useful for performing genetic or chemical screens for modulators of behavior.

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Section: Methodsmentioning

confidence: 99%

“…The image analysis software also employs a Mask-Region Convolutional Neural Network (Mask-RCNN) to automatically annotate and enumerate worm embryos in each well (Figs. 1 F and G) (30,31).…”

Section: Methods)mentioning

confidence: 99%

Automated multimodal imaging ofCaenorhabditis elegansbehavior in multi-well plates

Ji,

Chen,

Fang-Yen

2024

Preprint

Self Cite

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“…For decades, biomedical engineers have automated the manipulation of droplets, 51 cells, 52,53 colonies, 54 embryos, 55 and worms. 56 Electrostatic, 57 magnetic, 58 acoustic, 59 and pneumatic soft 60 end-effectors have been tethered to a robotic arm to manipulate small objects. For instance, Drury and Dembo 61 examined the hydrodynamics of human neutrophils during micropipette aspiration, and Kumagai and Fuchiwaki 62 developed a capillary dispenser that could pick-and-place objects.…”

Section: Microtissue Pick-and-place Using a Microfluidic 'Lift'-and-t...mentioning

confidence: 99%

Low-Cost Robotic Manipulation of Live Microtissues for Cancer Drug Testing

Stepanov,

Gottshall,

Ahmadianyazdi

et al. 2024

Preprint

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The small amount of human tissue available for testing is a paramount challenge in cancer drug development, cancer disease models, and personalized oncology. Technologies that combine the microscale manipulation of tissues with fluid handling offer the exciting possibility of miniaturizing and automating drug evaluation workflows. This approach minimizes animal testing and enables inexpensive, more efficient testing of samples with high clinical biomimicry using scarce materials. We have developed an inexpensive platform based on an off-the-shelf robot that can manipulate microdissected tissues (µDTs) into user-programmed positions without using intricate microfluidic designs nor any other accessories such as a microscope or a pneumatic controller. The robot integrates complex functions such as vision and fluid actuation by incorporating simple items including a USB camera and a rotary pump. Through the robot′s camera, the platform software optically recognizes randomly-seeded µDTs on the surface of a petri dish and positions a mechanical arm above the µDTs. Then, a custom rotary pump actuated by one of the robot′s motors generates enough microfluidic lift to hydrodynamically pick and place µDTs with a pipette at a safe distance from the substrate without requiring a proximity sensor. The platform′s simple, integrated construction is cost-effective and compact, allowing placement inside a tissue culture hood for sterile workflows. The platform enables users to select µDTs based on their size, place them in user-programmed arrays, such as multi-well plates, and control various robot motion parameters. As a case application, we use the robotic system to conduct semi-automated drug testing of mouse and human µDTs in 384-well plates. Our user-friendly platform promises to democratize microscale tissue research to clinical and biological laboratories worldwide.

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A robotic system for automated genetic manipulation and analysis ofCaenorhabditis elegans

Cited by 2 publications

References 65 publications

Automated multimodal imaging ofCaenorhabditis elegansbehavior in multi-well plates

Automated multimodal imaging ofCaenorhabditis elegansbehavior in multi-well plates

Low-Cost Robotic Manipulation of Live Microtissues for Cancer Drug Testing

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