ABSTRACT
As three-dimensional microscopy becomes commonplace in biological research, there is an increasing need for researchers to be able to view experimental image stacks in a natural three-dimensional viewing context. Through stereoscopy and motion tracking, commercial virtual reality headsets provide a solution to this important visualization challenge by allowing researchers to view volumetric objects in an entirely intuitive fashion. With this motivation, we present DIVA, a user-friendly software tool that automatically creates detailed three-dimensional reconstructions of raw experimental image stacks that are integrated in virtual reality. In DIVA's immersive virtual environment, users can view, manipulate and perform volumetric measurements on their microscopy images as they would to real physical objects. In contrast to similar solutions, our software provides high-quality volume rendering with native TIFF file compatibility. We benchmark the software with diverse image types including those generated by confocal, light-sheet and electron microscopy. DIVA is available at https://diva.pasteur.fr and will be regularly updated.
Subject(s)
Imaging, Three-Dimensional/instrumentation , Virtual Reality , Humans , Microscopy , Software , User-Computer InterfaceABSTRACT
Virtual reality (VR) has recently become an affordable technology. A wide range of options are available to access this unique visualization medium, from simple cardboard inserts for smartphones to truly advanced headsets tracked by external sensors. While it is now possible for any research team to gain access to VR, we can still question what it brings to scientific research. Visualization and the ability to navigate complex three-dimensional data are undoubtedly a gateway to many scientific applications; however, we are convinced that data treatment and numerical simulations, especially those mixing interactions with data, human cognition, and automated algorithms will be the future of VR in scientific research. Moreover, VR might soon merit the same level of attention to imaging data as machine learning currently has. In this short perspective, we discuss approaches that employ VR in scientific research based on some concrete examples.
Subject(s)
Virtual Reality , Algorithms , Cognition/physiology , Humans , Imaging, Three-Dimensional/methodsABSTRACT
Biomolecules are complex machines that are optimized by evolution to properly fulfill or contribute to a variety of biochemical tasks in the cellular environment. Computer simulations based on quantum mechanics and atomistic force fields have been proven to be a powerful microscope for obtaining valuable insights into many biological, physical, and chemical processes. Many interesting phenomena involve, however, a time scale and a number of degrees of freedom, notably if crowding is considered, that cannot be explored at an atomistic resolution. To bridge the gap between reality and simulation, many different advanced computational techniques and coarse-grained (CG) models have been developed. Here, we report some applications of the CG OPEP protein model to amyloid fibril formation, the response of catch-bond proteins to two types of fluid flow, and interactive simulations to fold peptides with well-defined 3D structures or with intrinsic disorder.
Subject(s)
Amyloid beta-Peptides/chemistry , Models, Molecular , Adhesins, Escherichia coli/chemistry , Adhesins, Escherichia coli/metabolism , Amyloid beta-Peptides/metabolism , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/metabolism , Fimbriae Proteins/chemistry , Fimbriae Proteins/metabolism , Molecular Dynamics Simulation , Monte Carlo Method , Protein FoldingABSTRACT
Inspired by the recent success of scientific-discovery games for predicting protein tertiary and RNA secondary structures, we have developed an open software for coarse-grained RNA folding simulations, guided by human intuition. To determine the extent to which interactive simulations can accurately predict 3D RNA structures of increasing complexity and lengths (four RNAs with 22-47 nucleotides), an interactive experiment was conducted with 141 participants who had very little knowledge of nucleic acids systems and computer simulations, and had received only a brief description of the important forces stabilizing RNA structures. Their structures and full trajectories have been analyzed statistically and compared to standard replica exchange molecular dynamics simulations. Our analyses show that participants gain easily chemical intelligence to fold simple and nontrivial topologies, with little computer time, and this result opens the door for the use of human-guided simulations to RNA folding. Our experiment shows that interactive simulations have better chances of success when the user widely explores the conformational space. Interestingly, providing on-the-fly feedback of the root mean square deviation with respect to the experimental structure did not improve the quality of the proposed models.
Subject(s)
Computer Simulation , RNA Folding , RNA , Access to Information , Feedback, Psychological , Humans , Internet , Models, Genetic , Models, Molecular , RNA/chemistry , Software , Solvents/chemistryABSTRACT
Tools on the theme of depression have been developed as part of the MobiQual programme which aims to improve the quality of professional practices in geriatric and gerontology facilities and in patients' homes. The scientific and pedagogical content was created by multi-disciplinary and multi-professional task forces, with the participation of the relevant national federations.
Subject(s)
Depression/therapy , Home Care Services , Quality Assurance, Health Care , Suicide Prevention , Aged , Depression/psychology , France , HumansABSTRACT
The Nutrition Domicile tool was developed as part of the MobiQual programme which aims to improve the quality of professional practices in geriatric and gerontological institutions and at home. Its pedagogical content was drawn up by a multi-disciplinary and multi-professional taskforce, with the participation of the main federations from the home care sector.
Subject(s)
Geriatric Assessment , Home Care Services , Nutrition Assessment , Aged , France , Humans , Malnutrition/prevention & controlABSTRACT
The MobiQual programme aims to improve the quality of care through the use of pedagogical tools focused on public health issues. Developed by the French society of geriatrics and gerontology, and initially aimed at institutions, in 2009 the programme was opened up to those who provide home care. The "Pain, Well Treatment, Home" tool was the first to be specifically aimed at this sector
