Study Of Spatial Biological Systems Using a Graphical User Interface

Proceedings of the Tenth International Conference on Human-Computer Interaction, Crete, Greece, 22-27 June 2003In this paper, we describe a Graphical User Interface (GUI) designed to manage large quantities of image data of a biological system. After setting the design requirements for the system, we developed an ecology quantification GUI that assists biologists in analysing data. We focus on the main features of the interface and we present the results and an evaluation of the system. Finally, we provide some directions for some future work

Analysis of dynamic mechanical response in torsion

We investigate the dynamic response of industrial rubbers (styrene-butadiene random copolymers, SBR) in torsion and compare against common small amplitude oscillatory shear measurements by using a torsion rectangular fixture, a modified torsion cylindrical fixture, and a conventional parallel plate fixture, respectively, in two different rheometers (ARES 2kFRTN1 from TA Instruments, USA and MCR 702 from Anton Paar-Physica, Austria). The effects of specimen geometry (length-to-width aspect ratio) on storage modulus and level of clamping are investigated. For cylindrical specimens undergoing torsional deformation, we find that geometry and clamping barely affect the shear moduli, and the measurements essentially coincide with those using parallel plates. In contrast, a clear dependence of the storage modulus on the aspect ratio is detected for specimens having rectangular cross section. The empirical correction used routinely in this test is based on geometrical factors and can account for clamping effects, but works only for aspect ratios above a threshold value of 1.4. By employing a finite element analysis, we perform a parametric study of the effects of the aspect ratio in the cross-sectional stress distribution and the linear viscoelastic torsional response. We propose a new, improved empirical equation for obtaining accurate moduli values in torsion at different aspect ratios, whose general validity is demonstrated in both rheometers. These results should provide a guideline for measurements with different elastomers, for which comparison with dynamic oscillatory tests may not be possible due to wall slip issues

Fast, automated measurement of nematode swimming (thrashing) without morphometry

Background: The "thrashing assay", in which nematodes are placed in liquid and the frequency of lateral swimming ("thrashing") movements estimated, is a well-established method for measuring motility in the genetic model organism Caenorhabditis elegans as well as in parasitic nematodes. It is used as an index of the effects of drugs, chemicals or mutations on motility and has proved useful in identifying mutants affecting behaviour. However, the method is laborious, subject to experimenter error, and therefore does not permit high-throughput applications. Existing automation methods usually involve analysis of worm shape, but this is computationally demanding and error-prone. Here we present a novel, robust and rapid method of automatically counting the thrashing frequency of worms that avoids morphometry but nonetheless gives a direct measure of thrashing frequency. Our method uses principal components analysis to remove the background, followed by computation of a covariance matrix of the remaining image frames from which the interval between statistically-similar frames is estimated. Results: We tested the performance of our covariance method in measuring thrashing rates of worms using mutations that affect motility and found that it accurately substituted for laborious, manual measurements over a wide range of thrashing rates. The algorithm used also enabled us to determine a dose-dependent inhibition of thrashing frequency by the anthelmintic drug, levamisole, illustrating the suitability of the system for assaying the effects of drugs and chemicals on motility. Furthermore, the algorithm successfully measured the actions of levamisole on a parasitic nematode, Haemonchus contortus, which undergoes complex contorted shapes whilst swimming, without alterations in the code or of any parameters, indicating that it is applicable to different nematode species, including parasitic nematodes. Our method is capable of analyzing a 30 s movie in less than 30 s and can therefore be deployed in rapid screens. Conclusion: We demonstrate that a covariance-based method yields a fast, reliable, automated measurement of C. elegans motility which can replace the far more time-consuming, manual method. The absence of a morphometry step means that the method can be applied to any nematode that swims in liquid and, together with its speed, this simplicity lends itself to deployment in large-scale chemical and genetic screens. </p

Assessing motor-related phenotypes of Caenorhabditis elegans with the wide field-of-view nematode tracking platform

Caenorhabditis elegans is a valuable model organism in biomedical research that has led to major discoveries in the fields of neurodegeneration, cancer and aging. Because movement phenotypes are commonly used and represent strong indicators of C. elegans fitness, there is an increasing need to replace manual assessments of worm motility with automated measurements to increase throughput and minimize observer biases. Here, we provide a protocol for the implementation of the improved wide field-of-view nematode tracking platform (WF-NTP), which enables the simultaneous analysis of hundreds of worms with respect to multiple behavioral parameters. The protocol takes only a few hours to complete, excluding the time spent culturing C. elegans, and includes (i) experimental design and preparation of samples, (ii) data recording, (iii) software management with appropriate parameter choices and (iv) post-experimental data analysis. We compare the WF-NTP with other existing worm trackers, including those having high spatial resolution. The main benefits of WF-NTP relate to the high number of worms that can be assessed at the same time on a whole-plate basis and the number of phenotypes that can be screened for simultaneously