Table 1.
Overview of machine and tool build resources.
Fig 1.
Tools designed and implemented for duckweed growth assays.
(a) An inoculation loop tool. Different inoculation loops can be manually swapped into the same tool holder. (b) A 50cc syringe. (c) A side-facing camera to image parallel to the deck of the machine. (d) A top-down camera to image wells and other objects on the deck of the machine. (e) A 10cc syringe. Created with BioRender.com.
Fig 2.
A Jubilee compatible OT-2 pipette tool.
(a) The tool is designed with an external limit switch, located behind the 3D printed frame inside of the orange region of interest. (b) When pushed upwards, the toolplate is designed to translate vertically, activating the limit switch. Note the compressed flexure. (c) A magnified side-view of the uncompressed flexure. The limit switch, highlighted in orange, is not pressed. (d) A magnified side-view of the compressed flexure. The limit switch makes contact with the toolplate, signalling application of the pipette tip.
Fig 3.
(a) The tool is first aligned to an available pipette tip. This process is handled by our Python modules. (b) The Jubilee platform moves upwards until a limit switch is activated. (c) The pipette tip is properly applied to the tool.
Fig 4.
Graphical overview of the automated growth assay workflow implemented by the Duckbot.
(a) The Duckbot is a Jubilee multi-tool changing motion platform outfitted with tools and associated software for duckweed handling. (b) A lab automation deck attachment is installed on the machine which supports six standard size well plates to be inserted. By default, our software assumes the first available position will be used for media reservoirs, marked R, and the other positions are available for well plates. This setup is configurable. (c) Relevant media reservoirs for our duckweed assays are petri dishes filled with duckweed or growth media. We use 24-well plates as our primary labware in our examples. (d) The Duckbot is outfitted with tools including a top-down camera which images the bed plate, a side-facing camera, an inoculation loop holder, a 10cc syringe, a 50cc syringe, and an OT-2 P300 pipette. The Duckbot can switch between these tools; inactive tools are parked along the back rail of the machine. (e) We scaffold our growth assay with a set of Jupyter notebooks which make use of our custom machine and tool control libraries. The notebooks are run using a Raspberry Pi. Created with BioRender.com.
Fig 5.
Overview of the growth assay workflow.
(a) An overhead image of the Duckbot. Tools are parked along the rear rail of the machine. A deck attachment houses well plates and media reservoirs; tools can be picked up and changed to manipulate materials installed in the bed. (b) A 50cc syringe tool fills wells with relevant media given an experimental definition. (c) Duckweed fronds are picked up and transferred using inoculation loops, among other tools.
Fig 6.
Setting up experimental well plates with the Duckbot.
(a) The software visualizes the experimental setup. The first (of three) 24-well plates is shown, with different media and duckweed strains labeled. Given the experimental setup, the Jupyter notebook will guide the operator through machine setup. In this case, the three well plates are loaded into the relevant bed plate position. (b) The lab automation deck offers six slots which can be installed with various labware. Shown here is a reservoir of duckweed, an OpenTrons pipette tip rack, and 6-, 24-, and 96-well plates. A 3D printed attachment houses a sharps container.
Fig 7.
Evaluating duckweed transfer options.
Three tools were tested including a standard inoculation loop, a custom 3D printed inoculation loop whose loop is at a right angle to the handle, and a 10cc syringe. Inoculation loops were simply dipped into the duckweed reservoir; the syringe was used in conjunction with the camera tool to identify an individual frond to aspirate. Each tool can be used as a part of a closed loop wherein transfer success is confirmed using the camera tool, and automatically retried on failures. Created with BioRender.com.
Fig 8.
Image collection and analysis.
(a) The top-down camera tool is used to image individual wells. (b) Example images over a 1-week period track the growth of Lemna minor (top), Spirodela polyrhiza (middle), and Wolffia australiana (bottom).
Fig 9.
Growth curves for each duckweed genotype.
Frond area over time is presented for each of our four duckweed genotypes under each media regime.
Fig 10.
Jubilee as an open platform for automation of laboratory research.
New tools and a software can be integrated into the tool-changing system to enable novel experiments. The experimental results can then be used to motivate new tool development for subsequent experiments. The resulting tools and software can be shared back into the community for reproduction and extension by others. Created with BioRender.com.