How to build your own Rhizotron Camera

Minirhizotron cameras are systems developed to obtain images from the soil biological activity (roots growth in particular, cf Fig. 1). Minirhizotron cameras are expansive pieces of equipment (approx £15000), although they are quite simple systems to design. There are however very cheap pieces of hardware that can be used to build such equipments. In this document, I explain how to build your own cheap minirhizotron camaras using a standard webcam. 

 

 

 

 

 

 RhizoCam principle

 Figure 1: example of a minirhizotron experimental setup: a camera is placed in a transparent tube to image below ground structures. Images are collected through a 45° angle mirror to collect images perpendicular to the faces of the plastic tubes

Image acquisition device: Rhizotron cameras can be built using web cams with manual focus. These cameras allow imaging with reduced focal distance (around 1cm). There are now web cams with better lens (e.g. Logitech has glass lenses and sometime Zeiss objectives). This makes images of reasonable quality for an affordable price (£20-£70). The position of the camera can be either directly perpendicular to tube and collect images directly. This solution allows images of higher magnification and less image distortion due to the non planar surfaces of rhizotron tubes. Alternatively, the focal distance can be increased by using a 45° mirror angle. In each case, the manual focus needs to be set up to obtain properly focused images.

Illumination: A good illumination is important to obtain clear images and good contrast between soil and roots. We used normal white leds to build a “belt”of light (Fig 2B) and we tape them on the web cam. There are also UV leds and these could be combined with white light led to segment living roots. Leds are also very cheap (<£1).

Acquisition program: Web cams are easy to program. I’ve made a simple interface to trigger the capture of images and naming of images using the python programming languages and videcapture python library (http://videocapture.sourceforge.net/). There are other common python libraries to capture images from webcam such as pygame. The program can be downloaded here:

rhizo_cam.zip

Building the frame: The frame can be build out of plastic plumbing pipes (Fig 2C-D). A wooden pole is fixed with screws to the plastic tubes and the end of the tube is cut to fit the camera. There are different diameters both of plastic rhizotron tubes and plumbing pipes. In order to adjust the diameter of the frame to the rhizotron tube diameter, an additional section of tube can be split axially on one side and placed externally to envelop the inner tube. This allows also embedding the screws used for fixing the pole as well. The whole construction is covered with a tissue reduce friction.

Calibrating the camera: To determine the physical size of the images captured, one can place a graduated millimetre ruler under the camera. If the focus of the camera has not been changed, the camera should focus at the same distance than when in the rhizotron tube. Image processing software can then be used to determine the physical size of your pixels in the image using measure tools in imageJ for example.

 RhizoCam construction
 Figure 2: Building of a cheap minirhizotron camera. (A) a web cam is used (here the bottom of the frame has been removed to obtain sufficient focal distance). (B) A LED “belt” is assembled and is then taped on the border of the webcam. (C) This is then assembled on a chassis made of plumbing plastic tubes fixed on a wooden pole. (D) A second tube is split longitudinally to envelop the inner tube holding the equipment, and a tissue is used to wrap the whole system.

 

Simple software to measure root length
I have made this simple software to measure root length from images collected by the program for the capture of images. It consist of a graphical interface that lets you draw lines on the image and recod the coordinates and image ID to write data files.
You can download the code here:

Processing script