Nicolás Gaggion¹, Federico Ariel², Vladimir Daric³, Éric Lambert³, Simon Legendre³, Thomas Roulé³, Alejandra Camoirano², Diego Milone¹, Martin Crespi³, Thomas Blein³, Enzo Ferrante¹

¹ Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe, Argentina.
² Instituto de Agrobiotecnología del Litoral (IAL), CONICET, FBCB, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, Santa Fe, Argentina.
³ Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Saclay and University of Paris Bâtiment 630, 91192 Gif sur Yvette, France.

The hardware (3D print and laser cut) of the ChronoRoot module designed for image-based plant phenotyping.

The ChronoRoot device is an affordable and modular imaging system based on 3D-printed and laser cut pieces and off-the-shelf electronics. Each module consists of a Raspberry Pi (v3)-embedded computer controlling four fixed-zoom and fixed-focus cameras (RaspiCam v2), and an array of infrared (IR) LED back-light. In between each camera and the corresponding IR array, there is a vertical 12 x 12 cm plate for seedling growth, allowing automatic image acquisition repeatedly along the experiment without any modification or movement of the imaging setup. The four-plate module is small (62 x 36 x 20 cm) and can be placed in any growth chamber. The different parts of the imaging setup (back-light, plate support and camera) can be positioned along a horizontal double-rail to control the field of view of the camera and accurate lightning. In addition, the camera can be moved vertically. ChronoRoot allows image acquisition at a high temporal resolution (a set of pictures every minute). The use of an IR back-light (850 nm) and optional long pass IR filters (> 830 nm) allow acquiring images of the same quality independently from the light conditions required for the experiment, during day and night.

In this repository, we include the hardware specification and the 3D printing and laser cutting files needed to build a module. These notes and files are provided as open-hardware specifications (CERN Open Hardware Licence version 2), to encourage other scientists to 3D print and mount the device in their own laboratories.

The module consist of a Raspberry Pi 3 model B with an additional camera multiplexer module (IVPort V2 Raspberry Pi Camera Module V2 Multiplexer, Ivmech Mekatronik & İnovasyon Ltd.) and allows to connect four cameras. It is boxed in a cage fixed under the main board.

(A) mobile and controlled infrared (IR) backlight (850 nm), (B) mobile plate support, (C) diffusing filter, (D) 12 cm x 12 cm square plate with QR code on the top, (E) Camera case equipped with an IR long pass filter (> 830 nm), (F) mobile camera support, (G) Raspberry Pi computer controlling the module (IR backlight and camera). The NIR illumination was build with four rows of LED flexible tape (tri-chip SMD5050-150-IR 850 nm, Huake LTD, China) fixed in a sandwich between two acrylic plates (580 mm x 140 mm x 3 mm) laser cuts to allow air flow and prevent the LED strip from ungluing. The four strips of LED were connected in parallel to a 12V AC/DC adaptor fixed under the module. The power supply cable of the adaptor is under the control of relay (Single Relay Board #27115, Parallax Inc), in a box fixed near the adaptor. It allows the control of the NIR illumination by the computer. The LED array is maintained vertically by L-shaped supports able to move along the aluminum horizontal axes as four individual panels in the module, corresponding to the respective plant plates.

Front view (left) and back view (right). The LED strips (D) are squeezed in between two acrylic panels (A and B) to prevent them from unsticking from the back panel. The strips are linked in parallel to the AC/DC adaptor through strip connector (C). The full LED panel is kept in vertical position via an L-shaped support (E) able to move along the double aluminum axis (F). Acrylic screws and nuts are used to maintain the LED panel on the L-shape support and fixed the horizontal position on the horizontal axis. U-shaped plate holders were designed to hold 12.5 cm x 12.5 cm square petri dishes used to grow the plants. The plate holder carries a diffusion filter (Cinegel R3000 Tough Rolux, Rosco Laboratories Inc.) at the back of the plate to allow homogeneous backlight illumination of the plates by the NIR LED array. The four plate holders can be moved independently along their respective horizontal axis.

Annotated 3D rendering (left) and picture (right) of the plate support. The U-shaped plate support (A) carries a diffusion filter at the back (B) allowing an homogeneous near-infrared illumination. Each support moves horizontally on the double axis (C). A classical 12.5 cm x 12.5 cm square plate fit into the plate support (E). Each camera is a regular Raspberry Pi NoIR V2 module (Sony IMX219 8-megapixel sensor) which is able to capture NIR wavelengths in addition to the classical visible spectrum. It is positioned in a box that can be moved vertically on an L-shaped support which can be shifted along the horizontal axis. The focus of the camera is adjusted manually before the start of the experiment by turning the objective lens using the provided crown. To be able to record pictures exclusively from the NIR spectrum, an IR long pass filter (12.5 mm diameter, RG830 Schott AG) can be positioned in front of the camera to exclude light below 830 nm and provide consistent images independently of the lightning of the growth chamber.

(Left) annotated 3D rendering; (middle) camera on a module carrying a filter; (right) camera on a module without the filter. A Raspberry Pi NoIR V2 module is enclosed in a 3D printed box (A) that could carry an optional filter (B). The box can be moved vertically on an L-shaped support (C) which itself is able to move along a double aluminum axis (F); The position of the L-shape support and of the camera box are secured by acrylic screw and nut (E for L-shaped support). The double aluminum axis is attached to the main board by a 3D printed part (D).

Schematic electric connection between the Raspberry Pi GPIO, the camera multiplexer, the relay board and AC/DC adaptor (up left). Real view of the connection with different part boxes open (right). The Raspberry Pi (B) is connected to a USB power adaptor (A). The camera multiplexer module (D) is plugged on the Raspberry Pi GPIO port and connected to the Raspberry Pi camera by a strip (C). Each camera is connected to the multiplexer by a strip (E). The pictures are saved on a USB stick (F) or a USB hard drive directly connected to the Raspberry Pi. A relay board (H) is connected to the Raspberry Pi GPIO and controls the main power (G) of the AC/Dc adaptor powering the LED strip. The final organization of the controlling part under the module main board raised by foots (J).

Software for image aquisition on the module available on the ChronoRoot Module Controler repository

Software for image analysis available on the ChronoRoot repository