Biomedical subjects

Jasmine Banks

Publications and source records attributed to Jasmine Banks.

3 recordsLinked to original sources

PubMed2006

SwarmPS: rapid, semi-automated single particle selection software.

Single particle analysis (SPA) coupled with high-resolution electron cryo-microscopy is emerging as a powerful technique for the structure determination of membrane protein complexes and soluble macromolecular assemblies. Current estimates suggest that approximately 10(4)-10(5) particle projections are required to attain a 3A resolution 3D reconstruction (symmetry dependent). Selecting this number of molecular projections differing in size, shape and symmetry is a rate-limiting step for the automation of 3D image reconstruction. Here, we present Swarm(PS), a feature rich GUI based software package to manage large scale, semi-automated particle picking projects. The software provides cross-correlation and edge-detection algorithms. Algorithm-specific parameters are transparently and automatically determined through user interaction with the image, rather than by trial and error. Other features include multiple image handling (approximately 10(2)), local and global particle selection options, interactive image freezing, automatic particle centering, and full manual override to correct false positives and negatives. Swarm(PS) is user friendly, flexible, extensible, fast, and capable of exporting boxed out projection images, or particle coordinates, compatible with downstream image processing suites.

Algorithms↗

PubMed2006

The discriminative bilateral filter: an enhanced denoising filter for electron microscopy data.

Advances in three-dimensional (3D) electron microscopy (EM) and image processing are providing considerable improvements in the resolution of subcellular volumes, macromolecular assemblies and individual proteins. However, the recovery of high-frequency information from biological samples is hindered by specimen sensitivity to beam damage. Low dose electron cryo-microscopy conditions afford reduced beam damage but typically yield images with reduced contrast and low signal-to-noise ratios (SNRs). Here, we describe the properties of a new discriminative bilateral (DBL) filter that is based upon the bilateral filter implementation of Jiang et al. (Jiang, W., Baker, M.L., Wu, Q., Bajaj, C., Chiu, W., 2003. Applications of a bilateral denoising filter in biological electron microscopy. J. Struc. Biol. 128, 82-97.). In contrast to the latter, the DBL filter can distinguish between object edges and high-frequency noise pixels through the use of an additional photometric exclusion function. As a result, high frequency noise pixels are smoothed, yet object edge detail is preserved. In the present study, we show that the DBL filter effectively reduces noise in low SNR single particle data as well as cellular tomograms of stained plastic sections. The properties of the DBL filter are discussed in terms of its usefulness for single particle analysis and for pre-processing cellular tomograms ahead of image segmentation.

Animals↗

PubMed2006

Virtual reality exposure therapy: 150-degree screen to desktop PC.

Virtual reality exposure therapy (VRET) developed using immersive or semi-immersive virtual environments present a usability problem for practitioners. To meet practitioner requirements for lower cost and portability VRET programs must often be ported onto desktop environments such as the personal computer (PC). However, success of VRET has been shown to be linked to presence, and the environment's ability to evoke the same reactions and emotions as a real experience. It is generally accepted that high-end virtual environments (VEs) are more immersive than desktop PCs, but level of immersion does not always predict level of presence. This paper reports on the impact on presence of porting a therapeutic VR application for schizophrenia from the initial research environment of a semi-immersive curved screen to PC. Presence in these two environments is measured both introspectively and across a number of causal factors thought to underlie the experience of presence. Results show that the VR exposure program successfully made users feel they were "present" in both platforms. While the desktop PC achieved higher scores on presence across causal factors participants reported they felt more present in the curved screen environment. While comparison of the two groups was statistically significant for the PQ but not for the IPQ, subjective reports of experiences in the environments should be considered in future research as the success of VRET relies heavily on the emotional response of patients to the therapeutic program.

Adolescent↗