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

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

Multi-imaging analysis of nascent surface structures generated during femtosecond laser irradiation of silicon in high vacuum

We report a correlative imaging analysis of a crystalline silicon target after irradiation with a low number of 1055 nm, similar to 850 fs laser pulses with several microscopy techniques (e.g., scanning electron microscopy, atomic force microscopy, Raman micro-imaging and confocal optical microscopy). The analysis is carried out on samples irradiated both in high vacuum and at atmospheric pressure conditions, evidencing interesting differences induced by the ambient environment. In high-vacuum conditions, the results evidence the formation of a halo, which is constituted by alternate stripes of amorphous and crystalline silicon, around the nascent ablation crater. In air, such an effect is drastically reduced, due to the significant back-deposition of nanoparticulate material induced by the larger ambient pressure