Eos rebel t5i camera

We utilized a Canon EOS REBEL T5i camera for image acquisition. Images were stored in the native RAW format. Substantial effort was put in to develop a standard imaging protocol (SIP) (Additional file 1) to ensure imaging consistency and quality. The flash function was kept off and an umbrella was always used to shade the area under the camera view in order to minimize illumination discrepancies between images. A light/color calibration protocol was also followed. An image of a color calibration chart (X-Rite ColorChecker Color Rendition Chart) was taken at the beginning of imaging operations, and every 20 min thereafter or whenever light condition changes (cloud cover, etc.). When taking pictures, the whole canopy was fit in the field of view of the camera. Weed control was practiced consistent with research plots and commercial farms; however, due to the small size of the field weed removal was done manually. Weeds in the view of camera were removed for enhanced efficiency of subsequent image processing. Images were taken across several days (at several times of the day) under various illumination conditions. Finally, the imaging protocol was chosen so that the imaging window and the camera resolution resulted in images with at least 6 pixels/mm, ensuring that the approach is transferable to other cameras that use an appropriate imaging window to get this resolution.

All images were analysed the same way, including images from Stynen et al. (2018) (link). Images of plates were taken with a EOS Rebel T5i camera (Canon, Tokyo, Japan) every two hours during the entire course of the PCA experiments. Incubation and imaging were performed in a spImager custom platform (S&P Robotics Inc, Toronto, Canada). We considered images after two days of growth for diploid selection plates and after four days of growth for DMSO and MTX plates. Images were analysed using gitter (R package version 1.1.1; Wagih and Parts, 2014 (link)) to quantify colony sizes by defining a square around the colony center and measuring the foreground pixel intensity minus the background pixel intensity.

Images were taken using a Canon EOS REBEL T5i camera with the Scene Intelligent Auto model. All images were stored in RAW image quality with a resolution of 5184 × 3456 (18 M). For consistent illumination, the flash function was kept off, and an umbrella was always used to shade the area under the camera view. A picture of the X-Rite Color Checker Color Rendition Chart was taken at the beginning of imaging operations and every 20 min thereafter or whenever the light condition changed (e.g., cloud cover) to calibrate the illumination of plant canopy images collected at that moment. When taking pictures, the whole canopy was fit in the field of view of the camera. Whenever possible, weeds and other plant residuals, connected to the plant canopy in the view of camera, were removed for easy image processing and enhanced efficiency of subsequent image processing. A detailed imaging protocol is shown in Box 1.