DICOM: key concepts--part II

The objective of these two installments of IT World was to give a general overview of DICOM and to take a look at different parts of the standard to get a sense of its main themes. We found that the standard provides a common reference for all developers but does not impose a single type of implementation. This allows for innovation. The standard is also built for flexibility, able to adapt to new modalities that have a need to communicate. The speedy acceptance of DICOM by the medical imaging industry is opening new possibilities for healthcare organizations to increase the quality while decreasing the cost of patient care. All of the DICOM networked supporting medical equipment as well as the organization's computer systems made by multiple original equipment manufacturers and located at one site or many sites can communicate by means of DICOM. This gives us the opportunity for medical images to be captured and communicated quicker. The result enables physicians to make diagnoses and treatment decisions sooner. It's all good stuff and even more reason why we should endeavor to understand the basics of DICOM. DICOM is here to stay!     

浅析PACS中的DICOM标准

随着医学影像设备的广泛应用以及PACS的快速发展,为了统一各种数字化影像设备的图像数据格式和数据传输标准而诞生的DICOM标准已经成为医学数字成像和通讯的共同标准。本文简要的介绍了DICOM标准的历史以及DICOM数据集和DICOM文件格式的组织形式。     

DICOM-RT Ion interface to utilize MC simulations in routine clinical workflow for proton pencil beam radiotherapy

To adopt Monte Carlo (MC) simulations as an independent dose calculation method for proton pencil beam radiotherapy, an interface that converts the plan information in DICOM format into MC components such as geometries and beam source is a crucial element. For this purpose, a DICOM-RT Ion interface (https://github.com/topasmc/dicom-interface) has been developed and integrated into the TOPAS MC code to perform such conversions on-the-fly. DICOM-RT objects utilized in this interface include Ion Plan (RTIP), Ion Beams Treatment Record (RTIBTR), CT image, and Dose. Beamline geometries, gantry and patient coordinate systems, and fluence maps are determined from RTIP and/or RTIBTR. In this interface, DICOM information is processed and delivered to a MC engine in two steps. A MC model, which consists of beamline geometries and beam source, to represent a treatment machine is created by a DICOM parser of the interface. The complexities from different DICOM types, various beamline configurations and source models are handled in this step. Next, geometry information and beam source are transferred to TOPAS on-the-fly via the developed TOPAS extensions. This interface with two treatment machines was successfully deployed into our automated MC workflow which provides simulated dose and LET distributions in a patient or a water phantom automatically when a new plan is identified. The developed interface provides novel features such as handling multiple treatment systems based on different DICOM types, DICOM conversions on-the-fly, and flexible sampling methods that significantly reduce the burden of handling DICOM based plan or treatment record information for MC simulations.     

Digital Imaging and Communications in Medicine (DICOM) information conversion procedure for SUV calculation of PET scanners with different DICOM header information

PurposeIn nuclear medicine, the standardized uptake value (SUV) obtained using positron emission tomography with 2-deoxy-2-fluoro-D-glucose (FDG-PET) is widely used as a semi-quantitative diagnosis factor. We found that the header file of the Philips Allegro PET scanner using the Digital Imaging and Communications in Medicine (DICOM) standard was stored differently than with other scanners. Thus, the purpose of this study was to develop a DICOM header information conversion program to ensure compatibility between Allegro and other equipment.Methods and resultsThe NEMA IEC Body phantom was scanned using the Allegro PET scanner. We conducted measurements and performed calculations by using commercial software and the proposed self-developed program, respectively, to compare the SUVs by using conversion data. The program consists of three parts: an input part that can load data regardless of the number of DICOM images, and conversion and output parts that can be used to convert the DICOM header information and store it in the order of slices. The results of the calculation are in good agreement with the data measured at 12 circular regions of interest. The percent difference was lower than the 20%.ConclusionIn conclusion, this study suggested a simple and convenient method to solve the incompatibility through conversion of the DICOM header information. This study thus provides physicians more accurate information for diagnosis and treatment.     

Protein synthesis during oxygen conformance and severe hypoxia in the mouse muscle cell line C2C12

Oxygen conformance can be described as the ability to reduce energy demand, and hence oxygen consumption, in response to a decline in oxygen availability without a decrease in the concentration of ATP. It has been proposed that oxygen conformance may enhance cellular survival at low oxygen concentrations. We demonstrate that non-contracting C2C12 cells, a mouse skeletal muscle cell line, are capable of oxygen conformance. Typically, we found oxygen consumption to decline by 30-40% as the concentration of oxygen was reduced from 100 microM to 10 microM. Unexpectedly, the rate of protein synthesis, a major energy consumer in the cell, did not decrease significantly during oxygen conformance. Unlike oxygen conformance, severe hypoxia (<0.5 microM) caused a 36% decline in the concentration of PCr, and under these conditions of energy stress, the rate of protein synthesis declined by 43%. We conclude that there are two distinct metabolic responses to declines in oxygen concentration in non-contracting C2C12 cells.     

Protein synthesis during oxygen conformance and severe hypoxia in the mouse muscle cell line C2C12

Oxygen conformance can be described as the ability to reduce energy demand, and hence oxygen consumption, in response to a decline in oxygen availability without a decrease in the concentration of ATP. It has been proposed that oxygen conformance may enhance cellular survival at low oxygen concentrations. We demonstrate that non-contracting C₂C₁₂ cells, a mouse skeletal muscle cell line, are capable of oxygen conformance. Typically, we found oxygen consumption to decline by 30–40% as the concentration of oxygen was reduced from 100 μM to 10 μM. Unexpectedly, the rate of protein synthesis, a major energy consumer in the cell, did not decrease significantly during oxygen conformance. Unlike oxygen conformance, severe hypoxia (<0.5 μM) caused a 36% decline in the concentration of PCr, and under these conditions of energy stress, the rate of protein synthesis declined by 43%. We conclude that there are two distinct metabolic responses to declines in oxygen concentration in non-contracting C₂C₁₂ cells.     

基于Visual C#语言的DICOM标准医学图像的显示和实现

介绍DICOM3.0医学图像文件的格式和C#语言的特点,首次利用Visual C#语言对该标准的图像进行显示和处理,能够直接读取DICOM格式原始图像数据,并可批量转换成BMP等格式进行处理,此项工作可为医学图像处理研究及相关医学图像软件开发奠定基础。     

基于PACS的医学图像压缩

从PACS和DICOM的定义出发,对基于PACS的医学图像压缩的要求和算法等方面作了阐述,还介绍了JPEG2000在医学图像压缩中的优势。     

A methodology to generate structured computational grids from DICOM data: application to a patient-specific abdominal aortic aneurysm (AAA) model

This study presents the generation of a multi-block structured grid on a real abdominal aortic aneurysm (AAA) acquired from Digital Imaging and Communication in Medicine (DICOM) data. With the use of a computed tomography exam (or medical images in standard DICOM format), the shape of a human organ is extracted and a structured computational grid is created. The structured grid generation is done by utilising Floater's and Gopalsamy et al.'s algorithm. The proposed methodology is applied to the AAA case, but it may also be applied to other human organs, enabling the scientist to develop an advanced patient-specific model. More importantly, the proposed methodology provides a precise reconstruction of the human organs, which is required in an AAA, where small variations in the geometry may alter the flow field, the stresses exerted on the walls and finally the rupture risk of the aneurysm.     

基于VT K 的D IC OM 医学图像三维重建研究

医学图像三维重建技术利用二维医学图像序列重建出三维模型,为医生提供直观、全面、准确的病灶和正常组织信息．是当今医学影像领域研究的热点之一。VTK是国际上广泛应用的可视化工具包,具有优秀的架构和运行机制。本文研究了DICOM3．0标准,提出了正确解读DICOM医学图像的方法;深入VTK内部机制,解决了VTK和DICOM医学图像读取模块间的数据接口问题;在三维重建过程中,为解决数据量巨大、成像时间漫长、阶梯效应、交互性不强等问题,重点剖析了VTK的数据处理机制。并给出相关优化方法。实验结果表明本文提出的解决方案和优化方法实用可靠,为进一步开发医学三雏图形系统打下了基础。     

A survey on non specialized off-the-shelf JPEG2000 viewers for digital microscopy use

The present paper will present a survey on features of a number of non-specialized off-the-shelf JPEG2000 viewers, seen from the point of view of digital microscopy. Selected viewers were tested within a number of usage scenarios, including: i) open a conformance test JPEG2000 file; ii) open a large JPEG2000 file; iii) moving from one point to another; iv) changing resolution/magnification. For each scenario, data recorded included: successful or unsuccessful operation; time needed for conclusion; occasional problems.Preliminary results demonstrate that JPEG2000 conformance as stated by many viewers is only limited to some of the possibilities of the JPEG2000 standard, in particular for what regards file size.     

Isolation and characterization of five dinucleotide microsatellite loci in the sandbar shark,Carcharhinus plumbeus

Five dinucleotide markers were isolated and optimized from a microsatellite‐enriched genomic library obtained from the sandbar shark, Carcharhinus plumbeus. Genotypic distributions of all markers were found to be in conformance with the expectations of Hardy–Weinberg equilibrium with four to 39 alleles present per locus. We amplified these loci in two female sharks and their litters. A maternal allele was recovered at each locus in all progeny indicating reliable amplification. More than two paternal alleles were recovered across both litters indicating genetic polyandry. Additionally, these markers were amplified across 10 carcharhiniform species to examine their utility in other studies.     

The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra

The Paragon Algorithm, a novel database search engine for the identification of peptides from tandem mass spectrometry data, is presented. Sequence Temperature Values are computed using a sequence tag algorithm, allowing the degree of implication by an MS/MS spectrum of each region of a database to be determined on a continuum. Counter to conventional approaches, features such as modifications, substitutions, and cleavage events are modeled with probabilities rather than by discrete user-controlled settings to consider or not consider a feature. The use of feature probabilities in conjunction with Sequence Temperature Values allows for a very large increase in the effective search space with only a very small increase in the actual number of hypotheses that must be scored. The algorithm has a new kind of user interface that removes the user expertise requirement, presenting control settings in the language of the laboratory that are translated to optimal algorithmic settings. To validate this new algorithm, a comparison with Mascot is presented for a series of analogous searches to explore the relative impact of increasing search space probed with Mascot by relaxing the tryptic digestion conformance requirements from trypsin to semitrypsin to no enzyme and with the Paragon Algorithm using its Rapid mode and Thorough mode with and without tryptic specificity. Although they performed similarly for small search space, dramatic differences were observed in large search space. With the Paragon Algorithm, hundreds of biological and artifact modifications, all possible substitutions, and all levels of conformance to the expected digestion pattern can be searched in a single search step, yet the typical cost in search time is only 2-5 times that of conventional small search space. Despite this large increase in effective search space, there is no drastic loss of discrimination that typically accompanies the exploration of large search space.     

Government regulation of nonhuman primate facilities

Myriad international, federal, and state laws, regulations, rules, guidelines, and standards directly affect the activities of all nonhuman primate research facilities. Federal regulations alone encompass every aspect of facility operations. They govern the procurement, possession, handling, care, and utilization of nonhuman primates, the design, construction, maintenance, and operation of the facility, and the occupational and environmental protection afforded not only facility personnel, but also the general public. Proper management of a nonhuman primate facility depends on continual monitoring of constantly changing laws and regulations applicable to the type of facility operated and research conducted. An in-house compliance assurance program is necessary to assure conformance with pertinent regulations.     

Reducing inter- and intra-planner variability in radiotherapy plan output with a commercial knowledge-based planning solution

PurposeThis study measured to which extent RapidPlan can drive a reduction of the human-caused variability in prostate cancer treatment planning.MethodsSeventy clinical prostate plans were used to train a RapidPlan model. Seven planners, with different levels of planning experience, were asked to plan a VMAT treatment for fifteen prostate cancer patients with and without RapidPlan assistance. The plans were compared on the basis of target coverage, conformance and OAR sparing. Inter-planner and intra-planner variability were assessed on the basis of the Plan Quality Metric formalism. Differences in mean values and InterQuartile Ranges between patients and operators were assessed.ResultsRapidPlan-assisted plans matched manual planning in terms of target coverage, homogeneity, conformance and bladder sparing but outperformed it for rectum and femoral heads sparing. 8 out of 15 patients showed a statistically significant increase in overall quality. Inter-planner variability is reduced in RapidPlan-assisted planning for rectum and femoral heads while bladder variability was constant. The inter-planner variability of the overall plan quality, IQR of PQM%, was approximately halved for all patients. RapidPlan assistance induced a larger increase in plan quality for less experienced planners. At the same time, a reduction in intra-planner variability is measured with a significant overall reduction.ConclusionsThe assistance of RapidPlan during the optimization of treatments for prostate cancer induces a significant increase of plan quality and a contextual reduction of plan variability. RapidPlan is proven to be a valuable tool to leverage the planning skills of less experienced planners ensuring a better homogeneity of treatment plan quality.     

常用医学图像“局部显微镜”程序的研究

在医学临床和科学研究中,常常需要将图像的某个感兴趣区域(ROI)进行放大显示,以便清晰地观察图像的细节.为了实现这一目标,采用IDL语言(Interactive Data Language)编写了应用程序,从而实现了医学图像“局部显微镜”的功能.一系列实验表明:对于各种常用的医学图像类型(灰度图像、RGB图像、DICOM图像等),程序均能较好地实现放大显示的功能.此外,该程序还具有人机交互性强、可移植性高等优点.     

A cloud-fog software architecture for dental CBCT dose monitoring using the DICOM structured report: Automated establishment of DRL

PurposeThe diagnostic reference level (DRL) has been established to optimize the diagnostic methods and reduce radiation dose during radiographic examinations. The aim of this study was to present a completely new solution based on Cloud-Fog software architecture for automatic establishment of the DRL values during dental cone-beam computed tomography (CBCT) according to digital imaging and communications in medicine (DICOM) structured reports.Methods and MaterialsA Cloud-Fog software architecture was used for automatic data handling. This architecture used the DICOM structured reports as a source for extracting the required information by fog devices in the imaging center. These devices transferred the derived information to the cloud server. The cloud server calculated the value of indication-based DRL in dental CBCT imaging based upon the parameters and adequate quantities of the absorbed dose. The feedback of DRL value was continuously announced to the imaging centers in 6 phases. In each phase, the level of the dose was optimized in imaging centers.ResultsThe DRL value was established for 5-specific indications, including third molar teeth (511 mGy.cm²), implant (719 mGy.cm²), form and position anomalies of the tooth (408 mGy.cm²), dentoalveolar pathologies (612 mGy.cm²), and endodontics (632 mGy.cm²). The determination of the DRL value in each phase revealed a downward trend until stabilization.ConclusionThe new solution presented in this study makes it possible to calculate and update the DRL value nationally and automatically among all centers. Also, the results showed that this approach is successful in establishing stabilized DRL values.     

容积减影成像计算机自动化技术与实现

探讨在PC机上对容积CT灌注（CTP）源影像全自动生成减影CTP源影像的方法。首先在WindowsXP操作系统中使用Matlab,对4层螺旋CTP源影像进行DICOM文件格式解析,获得CT成像设备的球管每转一周扫描层数及容积减影方法需要的其它参数信息,然后经过容积的CT值集合读、容积的CT值集合减以及容积的CT值集合写等几个步骤,生成减影CTP源影像的DICOM文件序列。使用该容积减影方法得到的减影CTP源影像,在定性肉眼观察和定量CT值矩阵比对上,与使用CT影像工作站上的减影软件手工逐层半自动减影得到的结果类同。容积减影方法实现了容积CTP源影像的自动化减影处理与成像,为最终形成一个一站式的减影CTP软件奠定了基础。     

Improving the biosafety of cell sorting by adaptation of a cell sorting system to a biosafety cabinet.

BACKGROUND: The jet-in-air cell sorters currently available are not very suitable for sorting potentially biohazardous material under optimal conditions because they do not protect operators and samples as recommended in the guidelines for safe biotechnology. To solve this problem we have adapted a cell sorting system to a special biosafety cabinet that satisfies the requirements for class II cabinets. With aid of this unit, sorting can be performed in conformance with the recommendations for biosafety level 2. METHODS: After integrating a modified fluorescence-activated cell sorter (FACS) Vantage into a special biosafety cabinet, we investigated the influence of the laminar air flow (LAF) inside the cabinet on side stream stability and the analytical precision of the cell sorter. In addition to the routine electronic counting of microparticles, we carried out tests on the containment of aerosols, using T4 bacteriophage as indicators, to demonstrate the efficiency of the biosafety cabinet for sorting experiments performed under biosafety level 2 conditions. RESULTS: The experiments showed that LAF, which is necessary to build up sterile conditions in a biosafety cabinet, does not influence the conditions for side stream stability or the analytical precision of the FACS Vantage cell sorting system. In addition, tests performed to assess aerosol containment during operation of the special biosafety cabinet demonstrated that the cabinet-integrated FACS Vantage unit (CIF) satisfies the conditions for class II cabinets. In the context of gene transfer experiments, the CIF facility was used to sort hematopoietic progenitor cells under biosafety level 2 conditions. CONCLUSIONS: The newly designed biosafety cabinet offers a practical modality for improving biosafety for operators and samples during cell sorting procedures. It can thus also be used for sorting experiments with genetically modified organisms in conformance with current biosafety regulations and guidelines.