数字化表达谱差异分析方法-DGE-P

目的：目前,关于数字化表达谱差异分析的方法及软件极少,且需懂得R语言等,操作繁琐,这给数字表达谱分析带来了不少困难,DGE-P软件针对数字化表达谱开发的差异分析软件。方法：DGE-P软件,利用倍数分析及数字化基因表达谱差异基因检测方法,对通过本软件标准化后的数据进行差异显著性分析。结果：DGE-P软件包含了丰度统计、数据标准化、求倍数分析和p-value值三个模块。可得出倍数分析与数字化基因表达谱差异基因检测方法（p-value）两个值。结论：DGE-P较以前的差异分析软件相比是一款针对数字化表达谱分析的软件,克服了其他软件在无重复实验数据时无法避免误差的缺陷。并且DGE-P较其他的软件相比使用方便,可在windows系统下运行,操作简单。     

Big forensic data reduction: digital forensic images and electronic evidence

An issue that continues to impact digital forensics is the increasing volume of data and the growing number of devices. One proposed method to deal with the problem of “big digital forensic data”: the volume, variety, and velocity of digital forensic data, is to reduce the volume of data at either the collection stage or the processing stage. We have developed a novel approach which significantly improves on current practice, and in this paper we outline our data volume reduction process which focuses on imaging a selection of key files and data such as: registry, documents, spreadsheets, email, internet history, communications, logs, pictures, videos, and other relevant file types. When applied to test cases, a hundredfold reduction of original media volume was observed. When applied to real world cases of an Australian Law Enforcement Agency, the data volume further reduced to a small percentage of the original media volume, whilst retaining key evidential files and data. The reduction process was applied to a range of real world cases reviewed by experienced investigators and detectives and highlighted that evidential data was present in the data reduced forensic subset files. A data reduction approach is applicable in a range of areas, including: digital forensic triage, analysis, review, intelligence analysis, presentation, and archiving. In addition, the data reduction process outlined can be applied using common digital forensic hardware and software solutions available in appropriately equipped digital forensic labs without requiring additional purchase of software or hardware. The process can be applied to a wide variety of cases, such as terrorism and organised crime investigations, and the proposed data reduction process is intended to provide a capability to rapidly process data and gain an understanding of the information and/or locate key evidence or intelligence in a timely manner.     

Accuracy of a remote quantitative image analysis in the whole slide images

The rationale for choosing a remote quantitative method supporting a diagnostic decision requires some empirical studies and knowledge on scenarios including valid telepathology standards. The tumours of the central nervous system [CNS] are graded on the base of the morphological features and the Ki-67 labelling Index [Ki-67 LI]. Various methods have been applied for Ki-67 LI estimation. Recently we have introduced the Computerized Analysis of Medical Images [CAMI] software for an automated Ki-67 LI counting in the digital images. Aims of our study was to explore the accuracy and reliability of a remote assessment of Ki-67 LI with CAMI software applied to the whole slide images [WSI]. The WSI representing CNS tumours: 18 meningiomas and 10 oligodendrogliomas were stored on the server of the Warsaw University of Technology. The digital copies of entire glass slides were created automatically by the Aperio ScanScope CS with objective 20x or 40x. Aperio's Image Scope software provided functionality for a remote viewing of WSI. The Ki-67 LI assessment was carried on within 2 out of 20 selected fields of view (objective 40x) representing the highest labelling areas in each WSI. The Ki-67 LI counting was performed by 3 various methods: 1) the manual reading in the light microscope - LM, 2) the automated counting with CAMI software on the digital images - DI , and 3) the remote quantitation on the WSIs - as WSI method. The quality of WSIs and technical efficiency of the on-line system were analysed. The comparative statistical analysis was performed for the results obtained by 3 methods of Ki-67 LI counting. The preliminary analysis showed that in 18% of WSI the results of Ki-67 LI differed from those obtained in other 2 methods of counting when the quality of the glass slides was below the standard range. The results of our investigations indicate that the remote automated Ki-67 LI analysis performed with the CAMI algorithm on the whole slide images of meningiomas and oligodendrogliomas could be successfully used as an alternative method to the manual reading as well as to the digital images quantitation with CAMI software. According to our observation a need of a remote supervision/consultation and training for the effective use of remote quantitative analysis of WSI is necessary.     

An image processing system for digital chest X-ray images

This paper investigates the requirements for image processing of digital chest X-ray images. These images are conventionally recorded on film and are characterised by large size, wide dynamic range and high resolution. X-ray detection systems are now becoming available for capturing these images directly in photoelectronic-digital form. In this report, the hardware and software facilities required for handling these images are described. These facilities include high resolution digital image displays, programmable video look up tables, image stores for image capture and processing and a full range of software tools for image manipulation. Examples are given of the application of digital image processing techniques to this class of image.     

高原鼠兔洞穴区次生斑块面积的测定方法

利用数码相机快速获得高原鼠兔挖掘活动形成的次生斑块图像,运用地理信息系统软件（Arcview） 计算其面积。运用该方法对草地内高原鼠兔洞穴区次生斑块的面积进行了实地测量,结果显示该方法可以快速、准确测量出不同形状次生斑块的面积,具有良好的实用性和可操作性。     

女性尿道阴道瘘数字化三维重建在临床治疗中的初步应用

目的:基于CT扫描图象建立精确的女性尿道阴道瘘数字化模型,探讨其在临床诊断及治疗中的应用。方法:选择1例女性尿道阴道瘘病例,进行尿道CT连续断层扫描,扫描结果导入Mimics软件中进行三维重建,利用三维重建模型指导临床。结果:建立女性尿道阴道瘘及周围结构的三维立体模型,可以方便地从任意角度和方向观察瘘管情况,测量有关的数据;还可以在数字化模型上进行手术设计。结论:女性尿道阴道瘘的数字化三维模型能够更直观、准确地反映病变部位的三维立体结构。对女性尿道阴道瘘的诊断、手术规划等有较大帮助。     

GelMap-a novel software tool for building and presenting proteome reference maps

Protein separation by two-dimensional gel electrophoresis is of central importance for proteomics. Upon combination with systematic protein identifications by mass spectrometry, large data sets are routinely generated in several proteome laboratories which can be used as "reference maps" for future analyses of analogous biochemical fractions. Here we present GelMap, a novel software tool for the building presentation and evaluation of proteomic reference maps. Variable frames are introduced in order to group proteins into functional categories on three levels or into categories according to differential abundance during comparative proteome analyses. The software is easy to handle as it only requires uploading two digital files to a web site. An additional file including detailed information on all proteins can be combined with the primary map. Two different gel-based projects are presented to illustrate the capacity of GelMap for proteome annotation and evaluation.     

CellProfiler: free, versatile software for automated biological image analysis

Careful visual examination of biological samples is quite powerful, but many visual analysis tasks done in the laboratory are repetitive, tedious, and subjective. Here we describe the use of the open-source software, CellProfiler, to automatically identify and measure a variety of biological objects in images. The applications demonstrated here include yeast colony counting and classifying, cell microarray annotation, yeast patch assays, mouse tumor quantification, wound healing assays, and tissue topology measurement. The software automatically identifies objects in digital images, counts them, and records a full spectrum of measurements for each object, including location within the image, size, shape, color intensity, degree of correlation between colors, texture (smoothness), and number of neighbors. Small numbers of images can be processed automatically on a personal computer and hundreds of thousands can be analyzed using a computing cluster. This free, easy-to-use software enables biologists to comprehensively and quantitatively address many questions that previously would have required custom programming, thereby facilitating discovery in a variety of biological fields of study.     

On-line data acquisition and evaluation of long-term measurements of circadian rhythms in individual cells of Acetabularia

A multitasking time-sharing computer system was implemented for studies of different circadian rhythms in individual cells of the unicellular green alga, Acetabularia. This fully automatized system allows simultaneous data acquisition and analysis. Graphical presentation of untreated and mathematically treated data is permanently available on three graphic displays and on a digital plotter. The sampling rate for the data acquisition in each of the 60 channels connected to the system is 720/24 h. Provisions have been made to guarantee uninterrupted data uptake for these long-term measurements by including an auto-restart module and by providing extremely reliable software for the experimenter using menu techniques.     

A GPU Simulation Tool for Training and Optimisation in 2D Digital X-Ray Imaging

Conventional radiology is performed by means of digital detectors, with various types of technology and different performance in terms of efficiency and image quality. Following the arrival of a new digital detector in a radiology department, all the staff involved should adapt the procedure parameters to the properties of the detector, in order to achieve an optimal result in terms of correct diagnostic information and minimum radiation risks for the patient. The aim of this study was to develop and validate a software capable of simulating a digital X-ray imaging system, using graphics processing unit computing. All radiological image components were implemented in this application: an X-ray tube with primary beam, a virtual patient, noise, scatter radiation, a grid and a digital detector. Three different digital detectors (two digital radiography and a computed radiography systems) were implemented. In order to validate the software, we carried out a quantitative comparison of geometrical and anthropomorphic phantom simulated images with those acquired. In terms of average pixel values, the maximum differences were below 15%, while the noise values were in agreement with a maximum difference of 20%. The relative trends of contrast to noise ratio versus beam energy and intensity were well simulated. Total calculation times were below 3 seconds for clinical images with pixel size of actual dimensions less than 0.2 mm. The application proved to be efficient and realistic. Short calculation times and the accuracy of the results obtained make this software a useful tool for training operators and dose optimisation studies.     

结合薄层CT技术建立下颌第一前磨牙三维有限元模型

目的结合薄层CT技术建立下颌第一前磨牙三维有限元模型。方法对正常人下颌第一前磨牙进行薄层CT扫描及图像处理,通过Matlab和ANSYS软件建立三维有限元模型,并加载验证模型力学分析的可行性。结果建立了包含髓腔的下颌第一前磨牙的三维有限元模型,得到101564个单元,144053个节点。载荷后的应力分布主要集中在颊尖部位和根尖部位,牙颈部受力较小。结论薄层CT技术与Matlab和ANSYS软件相结合,建立包含髓腔的下颌第一前磨牙的三维有限元模型,精度高、速度快,使用灵活,为后期的楔缺模型建立和分析奠定了基础。     

Issues in using whole slide imaging for diagnostic pathology: “routine” stains,immunohistochemistry and predictive markers

The traditional microscope, together with the “routine” hematoxylin and eosin (H & E) stain, remains the “gold standard” for diagnosis of cancer and other diseases; remarkably, it and the majority of associated biological stains are more than 150 years old. Immunohistochemistry has added to the repertoire of “stains” available. Because of the need for specific identification and even measurement of “biomarkers,” immunohistochemistry has increased the demand for consistency of performance and interpretation of staining results. Rapid advances in the capabilities of digital imaging hardware and software now offer a realistic route to improved reproducibility, accuracy and quantification by utilizing whole slide digital images for diagnosis, education and research. There also are potential efficiencies in work flow and the promise of powerful new analytical methods; however, there also are challenges with respect to validation of the quality and fidelity of digital images, including the standard H & E stain, so that diagnostic performance by pathologists is not compromised when they rely on whole slide images instead of traditional stained tissues on glass slides.     

The use of three-dimensional model construction of virtual technology in orthopedic treatment

ObjectiveThe objective of this study is to explore the construction of a digital three-dimensional model of virtual technology that plays an auxiliary role in orthopedic treatment.MethodsThree fracture patients were selected, with no abnormality was observed in bone examination, no musculoskeletal disease in the past; and spiral CT scan of the spine and pelvis, upper limbs, and lower limbs was performed. The virtual technology was used to build a digital 3D model, mainly using the editing software Mimics10.0 software. In addition, the virtual three-dimensional model was verified by virtual surgery, data storage security, work efficiency of the model, model validity, three-dimensional characteristics of the model, the interaction mode of the model, and the data accuracy of the model were studied.ResultsThe digital 3D model was successfully established by Mimics10.0 software. The data fitting efficiency was very high. The data storage security of the 3D model was greatly improved compared with the 2D model, and the work efficiency was improved by at least 50%. There was also a significant change in the accuracy and interaction of data acquisition. Therefore, the detection of digital 3D model work through virtual surgery simulation fully demonstrated the positive auxiliary role of 3D model in orthopedic treatment.ConclusionThe digital 3D model based on Mimics10.0 software is efficient and accurate in obtaining data. It is very effective for subsequent adjuvant therapy in the field of orthopedics, reducing the probability of misdiagnosis by doctors, saving time and improving efficiency, reducing patient's physical pain and unnecessary economic expenses.     

An evaluation of the analysis system of video transects used to sample subtidal epibiota

Two popular methods of benthic cover estimation (the point intercept technique with two sets of position points, and digital interactive color segmentation) were compared with an alternative method of digital cover estimation using Bezier curves as a tool for outlining the objects on an images and AutoCAD® software for the final evaluation of abundance. The comparison was done using still video images obtained from two 10-m transects on subtidal rocks off the Rimsky-Korsakov islands in the Sea of Japan (Russia). Ten rectangular sectors (1×0.4 m each) selected randomly within both video transects were analyzed. One-way ANOVA for repeated measurements was used to test the differences between methods. The point intercept technique differed significantly from both methods of digital estimation and had an essential positive bias. The Tukey multiple comparison test revealed the differences among digital estimation methods in the species, which have the complicated color with many contrast spots. The proposed approach using Bezier curves has an advantage over the interactive color segmentation if the objects under selection are lit at different levels or have a contrast coloration or are hidden by canopy organisms. Besides, estimation of cover in the field of AutoCAD® software is more precise and takes less time than that obtained using a scaled grid, available for automatically segmented species. The results showed that digital cover estimation using Bezier curves and AutoCAD® software is a convenient method for analyzing benthic samples at large spatial scales.     

Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography

In cryo-electron tomography (cryo-ET) of biological samples, the quality of tomographic reconstructions can vary depending on the transmission electron microscope (TEM) instrument and data acquisition parameters. In this paper, we present Parakeet, a ‘digital twin’ software pipeline for the assessment of the impact of various TEM experiment parameters on the quality of three-dimensional tomographic reconstructions. The Parakeet digital twin is a digital model that can be used to optimize the performance and utilization of a physical instrument to enable in silico optimization of sample geometries, data acquisition schemes and instrument parameters. The digital twin performs virtual sample generation, TEM image simulation, and tilt series reconstruction and analysis within a convenient software framework. As well as being able to produce physically realistic simulated cryo-ET datasets to aid the development of tomographic reconstruction and subtomogram averaging programs, Parakeet aims to enable convenient assessment of the effects of different microscope parameters and data acquisition parameters on reconstruction quality. To illustrate the use of the software, we present the example of a quantitative analysis of missing wedge artefacts on simulated planar and cylindrical biological samples and discuss how data collection parameters can be modified for cylindrical samples where a full 180° tilt range might be measured.     

On-line data acquisition and evaluation of long-term measurements of circadian rhythms in individual cells ofAcetabularia

A multitasking time-sharing computer system was implemented for studies of different circadian rhythms in individual cells of the unicellular green alga,Acetabularia. This fully automatized system allows simultaneous data acquisition and analysis. Graphical presentation of untreated and mathematically treated data is permanently available on three graphic displays and on a digital plotter. The sampling rate for the data acquisition in each of the 60 channels connected to the system is 720/24 h. Provisions have been made to guarantee uninterrupted data uptake for these long-term measurements by including an auto-restart module and by providing extremely reliable software for the experimenter using menu techniques.     

Using digital images to reconstruct three‐dimensional biological forms: a new tool for morphological studies

We examined two image‐based methods, photogrammetry and stereo vision, used for reconstructing the three‐dimensional form of biological organisms under field conditions. We also developed and tested a third ‘hybrid’ method, which combines the other two techniques. We tested these three methodologies using two different cameras to obtain digital images of museum and field sampled specimens of giant tortoises. Both the precision and repeatability of the methods were assessed statistically on the same specimens by comparing geodesic and Euclidean measurements made on the digital models with linear measurements obtained with caliper and flexible tape. We found no substantial difference between the three methods in measuring the Euclidean distance between landmarks, but spatially denser models (stereo vision and ‘hybrid’) were more accurate for geodesic distances. The use of different digital cameras did not influence the results. Image‐based methods require only inexpensive instruments and appropriate software, and allow reconstruction of the three‐dimensional forms (including their curved surfaces) of organisms sampled in the field. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 425–436.     

昆虫学多媒体信息获取与处理方法的初步研究

该文介绍了多媒体信息包括文字信息、音频信息、视频信息和图象信息的获取及其数字化制作技术。较详细地介绍了制作这些媒体资料所需的软硬件环境及具体的操作步骤。这里包括了文字的录入和处理;声音的录制和处理;数字视频的制作,包括昆虫摄像技术、各种来源的视频信息捕获、视频信息的处理等;数字图象的制作,包括昆虫的摄影技术、图象扫描、图象处理等。     

Open data and algorithms for open science in AI-driven molecular informatics

Recent years have seen a sharp increase in the development of deep learning and artificial intelligence-based molecular informatics. There has been a growing interest in applying deep learning to several subfields, including the digital transformation of synthetic chemistry, extraction of chemical information from the scientific literature, and AI in natural product-based drug discovery. The application of AI to molecular informatics is still constrained by the fact that most of the data used for training and testing deep learning models are not available as FAIR and open data. As open science practices continue to grow in popularity, initiatives which support FAIR and open data as well as open-source software have emerged. It is becoming increasingly important for researchers in the field of molecular informatics to embrace open science and to submit data and software in open repositories. With the advent of open-source deep learning frameworks and cloud computing platforms, academic researchers are now able to deploy and test their own deep learning models with ease. With the development of new and faster hardware for deep learning and the increasing number of initiatives towards digital research data management infrastructures, as well as a culture promoting open data, open source, and open science, AI-driven molecular informatics will continue to grow. This review examines the current state of open data and open algorithms in molecular informatics, as well as ways in which they could be improved in future.     

男性尿道直肠瘘数字化三维重建的初步应用

目的：基于CT扫描图象建立精确的男性尿道直肠瘘数字化模型,探讨其在临床诊断及治疗中的应用。方法：选择1例男性尿道直肠瘘病例,进行尿道CT连续断层扫描,扫描结果导入Mimics软件中进行三维重建,利用三维重建模型指导临床。结果：建立男性尿道直肠瘘及周围结构的三维立体模型,可以方便地从任意角度和方向观察瘘管情况,测量有关的数据;还可以在数字化模型上进行手术设计。结论：男性尿道直肠瘘的数字化三维模型能够更直观、准确地反映病变部位的三维立体结构。对男性尿道直肠瘘的诊断、手术规划等有较大帮助。