3D vision
The three dimensional image adquisition or reconstruction of animals with techniques like photogrammetry [1] is an important area of computer vision field. However, despite the fact that C. elegans image adquisition is a major part of most of the automatic systems that work with these nematodes for different purpose studies, the 3D imaging is mostly an unxplored and unused field due to the difficult of using the different existing techniques with the small scale of the target and the importance of the light conditions.
At the moment there are automated systems that work with different mutants, in different configurations of grown (multi-well, Petri dish,…) and for different aplications (life-span studies with individual tracking, fat studies with fluorescence, motility studies on microfluidic lab-on-a-chip devices,…) but in neither of them are used techniques of imaging or reconstruction in 3 dimensions even when they could add new information at the already existing models or create new ones.
There are, however, studies in which three dimensional images have been adquired or there have been a reconstruction from bidimensional images.
An example of this is the use of complex and expensive devices and equipment such as Light Sheet Microscopes, usually asociated with fluorescence experiments, or Optical Projection Tomography devices [2]. With these systems high resolution images can be obtained from different angles and using techniques like Multiview Deconvolution, optimized to reduce the convergence time dure to the data size, can achive a better resolution and contrast to improve the data adquisition and reconstruction [3].
Another example is using Atomic Force Microscopes to take three-dimensional images of C. elegans surface [4]. Or using Confocal Microscopes and reconstruct from the images took at different depths (Optical Sectioning) [5].
Figure 1: Atomic Force Microscope C. elegans imaging [4]
However, one of the most interesting aproaches , becase of its lower cost, complexity and the possibility of using at in vivo experiments, comes from the combination of traking systems along with stereo vision. This way, differemt samples of the nematode in different positions can be taken when traking the nematodes in a 3D media with a stereo pair, allowing a reconstruction and obtaining the information of the threedimensional model located in a concrete time [6][7].
Figure 2: Stereo Vision C. elegans reconstruction [6]
References
[1] S. M. Walker, A. L. R. Thomas, and G. K. Taylor, “Photogrammetric reconstruction of high-resolution surface topographies and deformable wing kinematics of tethered locusts and free-flying hoverflies,” J. R. Soc. INTERFACE, vol. 6, no. 33, pp. 351–366, 2009.
[2] M. Rieckher et al., “A Customized Light Sheet Microscope to Measure Spatio-Temporal Protein Dynamics in Small Model Organisms,” PLoS One, vol. 10, no. 5, pp. 1–15, 2015.
[3] S. Preibisch et al., “Efficient Bayesian-based multiview deconvolution,” Nat. Methods, vol. 11, no. 6, p. 645+, Jun. 2014.
[4] M. J. Allen, R. Kanteti, J. J. Riehm, E. El-Hashani, and R. Salgia, “Whole-animal mounts of Caenorhabditis elegans for 3D imaging using atomic force microscopy,” NANOMEDICINE-NANOTECHNOLOGY Biol. Med., vol. 11, no. 8, pp. 1971–1974, Nov. 2015.
[5] L. Chen, L. L. H. Chan, Z. Zhao, and H. Yan, “A novel cell nuclei segmentation method for 3D C. elegans embryonic time-lapse images,” BMC Bioinformatics, vol. 14, Nov. 2013.
[6] N. Kwon, J. Pyo, S.-J. Lee, and J. H. Je, “3-D Worm Tracker for Freely Moving C. elegans,” PLoS One, vol. 8, no. 2, pp. 1–6, 2013.
[7] N. Kwon, A. B. Hwang, Y.-J. You, S.-J. V. Lee, and J. Ho Je, “Dissection of C. elegans behavioral genetics in 3-D environments,” vol. 5, p. 9564, May 2015.