treegraph: automated drawing of complex tree figures using an extensible tree description format

treegraph assists in producing complex ready‐to‐publish figures of phylogenetic trees. The TGF format used by the program automates formatting of several different statistical support value types (confidence estimates) per tree node. Moreover, internal text and graphical labels are automatically arranged at the nodes as are annotations for clades or groups of terminals. treegraph imports nexus trees and related file formats. Beyond common tree edit operations, simultaneous pruning of subtrees (simplification of the tree to higher order clades) and saving of subtrees is possible. treegraph exports to the standard vector graphics formats Scalable Vector Graphics and PostScript.     

磁共振成像的三维图形定位的实现

在做磁共振成像时,根据需要医生应该能够对病人任意的解剖部位以及这个部位的任意方向进行扫描,为此需要得到扫描的中心位置、频率编码方向、相位编码方向等坐标信息。这个过程是比较繁琐的,我们开发出一个定位子系统,使得医生可以通过图形定位的方式来确定这套参数,做到所见即所得。     

A computational method for reliable gait event detection and abnormality detection for feedback in rehabilitation

In this paper, a gait event detection algorithm is presented that uses computer intelligence (fuzzy logic) to identify seven gait phases in walking gait. Two inertial measurement units and four force-sensitive resistors were used to obtain knee angle and foot pressure patterns, respectively. Fuzzy logic is used to address the complexity in distinguishing gait phases based on discrete events. A novel application of the seven-dimensional vector analysis method to estimate the amount of abnormalities detected was also investigated based on the two gait parameters. Experiments were carried out to validate the application of the two proposed algorithms to provide accurate feedback in rehabilitation. The algorithm responses were tested for two cases, normal and abnormal gait. The large amount of data required for reliable gait-phase detection necessitate the utilisation of computer methods to store and manage the data. Therefore, a database management system and an interactive graphical user interface were developed for the utilisation of the overall system in a clinical environment.     

A review of GPU-based medical image reconstruction

Tomographic image reconstruction is a computationally demanding task, even more so when advanced models are used to describe a more complete and accurate picture of the image formation process. Such advanced modeling and reconstruction algorithms can lead to better images, often with less dose, but at the price of long calculation times that are hardly compatible with clinical workflows. Fortunately, reconstruction tasks can often be executed advantageously on Graphics Processing Units (GPUs), which are exploited as massively parallel computational engines. This review paper focuses on recent developments made in GPU-based medical image reconstruction, from a CT, PET, SPECT, MRI and US perspective. Strategies and approaches to get the most out of GPUs in image reconstruction are presented as well as innovative applications arising from an increased computing capacity. The future of GPU-based image reconstruction is also envisioned, based on current trends in high-performance computing.     

Molecular Visualization on the Holodeck

Can virtual reality be useful for visualizing and analyzing molecular structures and three-dimensional (3D) microscopy? Uses we are exploring include studies of drug binding to proteins and the effects of mutations, building accurate atomic models in electron microscopy and x-ray density maps, understanding how immune system cells move using 3D light microscopy, and teaching schoolchildren about biomolecules that are the machinery of life. Virtual reality (VR) offers immersive display with a wide field of view and head tracking for better perception of molecular architectures and uses 6-degree-of-freedom hand controllers for simple manipulation of 3D data. Conventional computer displays with trackpad, mouse and keyboard excel at two-dimensional tasks such as writing and studying research literature, uses for which VR technology is at present far inferior. Adding VR to the conventional computing environment could improve 3D capabilities if new user-interface problems can be solved. We have developed three VR applications: ChimeraX for analyzing molecular structures and electron and light microscopy data, AltPDB for collaborative discussions around atomic models, and Molecular Zoo for teaching young students characteristics of biomolecules. Investigations over three decades have produced an extensive literature evaluating the potential of VR in research and education. Consumer VR headsets are now affordable to researchers and educators, allowing direct tests of whether the technology is valuable in these areas. We survey here advantages and disadvantages of VR for molecular biology in the context of affordable and dramatically more powerful VR and graphics hardware than has been available in the past.     

Computerised animal house management system (CAMS)

Data processing systems for the management of animal houses are available as individually tailored solutions to meet the specific requirements of different institutions in various sectors. After four years of use, a “proprietary system” (originally used by Boehringer/Mannheim), which was based on UNIFACE and ORACLE database software and consisted of a VAX station with eight terminals, was replaced by a PC-based multi-user system for administrative employees and animal technicians. The new system runs under the operating systems of Microsoft Windows 98 and Microsoft Windows NT and uses Microsoft Access 97 as the database software. A “multipurpose program system” was created in order to fulfil the following main functions: documentation and control of experimental plans and animal usage; registering changes in the number of animals available; controlling room use and animal storage areas; maintenance cost calculations for determining the cost of experiments and an evaluation of how animals are used and consumed.

CAMS (Computerised Animal House Management System) has a centralised / decentralised structure and is a user-friendly, interactive system which can only be accessed by authorised groups of users. You do not need to be highly skilled with computers to master the system. It can generate daily and monthly reports and any necessary documentation. Furthermore, it complies with the revised Animal Protection Act (1998; annual report on number of animals used), facilitates a detailed analysis of housing and the associated costs and provides options for documenting different types of experimental data.

For this reason, the system has become an increasingly important tool for the management of our own animal facilities and animal experiments as well as for external ones.     

Model-based approach for human kinematics reconstruction from markerless and marker-based motion analysis systems

Modeling tools related to the musculoskeletal system have been previously developed. However, the integration of the real underlying functional joint behavior is lacking and therefore available kinematic models do not reasonably replicate individual human motion. In order to improve our understanding of the relationships between muscle behavior, i.e. excursion and motion data, modeling tools must guarantee that the model of joint kinematics is correctly validated to ensure meaningful muscle behavior interpretation. This paper presents a model-based method that allows fusing accurate joint kinematic information with motion analysis data collected using either marker-based stereophotogrammetry (MBS) (i.e. bone displacement collected from reflective markers fixed on the subject's skin) or markerless single-camera (MLS) hardware. This paper describes a model-based approach (MBA) for human motion data reconstruction by a scalable registration method for combining joint physiological kinematics with limb segment poses. The presented results and kinematics analysis show that model-based MBS and MLS methods lead to physiologically-acceptable human kinematics. The proposed method is therefore available for further exploitation of the underlying model that can then be used for further modeling, the quality of which will depend on the underlying kinematic model.