A general purpose computerized display and analysis system for image processing in nuclear medicine.

In this work a general purpose image processor is described, which takes into account the special features and the various requirements for analysing images in nuclear medicine. A new approach for system structure involving encoding and representing medical images is given. This encoder, which is part of the image processor, is efficient especially for long-term storage and for certain pattern recognition in medical imaging. In this processor a statistical package is incorporated for collecting medical statistics using the acquired patient data. This information is used together with the encoder for an automated diagnostic system.     

Comparison of autofocus methods for automated microscopy

Traditional autofocus methods were designed for microscopes driven by single processor computers. As computers are developed that exploit massive parallelism when acquiring and analyzing images, parallel cellular logic techniques became available to focus automatically. This paper introduces the reader to both cellular logic techniques for autofocus and a new spectral moment autofocus measure. It then compares these methods with more traditional autofocus methods. It is shown that traditional methods based on measurements of image power-give the best results when tested on one set of real images and two sets of synthetic images. The next best methods are the cellular logic and spectral moment techniques, while the worst are those based on the image probability density function or histogram.     

Imaging system for morphometric assessment of absorption or fluorescence in stained cells

An image acquisition and processing system has been developed for quantitative microscopy of absorption or fluorescence in stained cells. Three different light transducers are used in the system to exploit the best characteristics of these sensors for different biological measurements. A digital scanner, in the form of a linear array charge-coupled device (CCD), acquires data with high spatial and photometric resolution. A color (RGB) camera is employed when spectral information is required for the segmentation of cellular subcomponents. An image-intensified charged-injection device (CID) camera provides for very low light intensity measurements, primarily for fluorescence-labeled cells. Properties of these transducers, such as contrast transfer function, linearity, and photo-response nonuniformity, have been measured. Two dedicated image processing units were incorporated into the system. The front-end processor, based on a digital signal processor, provides functions such as object detection, raw image calibration, compression, artifact removal, and filtering. The second image processor is associated with the frame memory and includes a histogram processor, a dedicated arithmetic logic unit for image processing functions, and a graphics module for one-bit overlay functions. An interactive program was developed to acquire cell images and to experiment with a range of segmentation algorithms, feature extractions, and other image processing functions. The results of any image operation are displayed on the video monitor. Once a desired processing sequence is determined, the sequence may be stored to become part of a command library and can be executed thereafter as a single instruction.     

Development of an imaging flow cytometer

A cell analyzer that combines the characteristics of image cytometry and flow cytometry is being designed and constructed at the University of Sydney. This paper describes the image acquisition and processing components and some preliminary applications. Cells stained by a fluorescent dye and suspended in a liquid medium are conveyed by a hydraulic system to a flow channel assembly, where they are detected and illuminated by a laser beam. A two-dimensional charge-coupled device is used to acquire the cell images. Image processing and classification is to be carried out by a special-purpose computer comprising an array of four conventional microprocessors and a highly parallel processor consisting of an array of 32 X 32 processing elements. The analyzer will be capable of using morphologic, immunologic and biochemical information to classify and sort up to 500 cells per second. Because of its unique characteristics, the instrument will be of particular use in tumor heterogeneity studies.     

Application of a small microcomputer to cell image analysis

Solutions to three problems in using small microcomputers for interactive cell image analysis are discussed. (1) To allow interactive processing of up to 62 X 88 pixels on inexpensive screens, data can be displayed in gray levels with an approximate logarithmic grading. Each pixel is composed of 32 screen coordinates, applying the dither matrix method to avoid artificial structures. (2) To mark special regions of interest in the image, a graphic cursor, handled from the keyboard, was implemented. (3) To evaluate parts of the image, as outlined by the cursor, the program must distinguish whether a particular pixel is outside, inside or on the border of the region. The developed algorithms permit practical interactive evaluation of cell images on a small microcomputer, with no image analysis implementation. However, it is necessary that the assembly language of the microprocessor be available for some sophisticated programming and that the operating system support graphic facilities with an appropriate resolution.     

Context-free spheres: A new method for rapid CPK image generation

A new algorithm for rendering CPK images of molecules is presented. The algorithm is based on the observation that (given certain assumptions) the appearance of a sphere representing an atom is independent of the atom's position or orientation. For example, the size of a sphere's projection on the viewing plane is independent of its distance from the viewing plane. The shading of a sphere is dependent only on lighting parameters that are identical for each atom type. This algorithm takes advantage of this observation by precomputing a template for each unique atom type and stamping these into the image with appropriate offsets in X, Y and Z. The implementation described herein enables generation of CPK images an order of magnitude faster than previous methods, with little sacrifice in image quality.     

A red line not to cross: Evaluating the limitation and properness of gel image tuning procedures

Currently, results of gel electrophoresis are commonly documented in digital formats by image acquisition instruments. In this study, gel images tuned by a common image processing software package, Photoshop, were assessed to understand the transforming algorithms and their impacts on quantitative analysis. TotalLab 100, an electrophoresis gel image analysis software package, was applied for image quantitation and evaluation. The three most frequently used image tuning functions—adjustments of the brightness, contrast, and grayscale span (level) of images—were investigated using both data generated from a standard grayscale tablet and an actual electrophoresis gel image. The influences of these procedures were analyzed for the grayscale transformation between the input and output images. Although all three procedures differentially improved the visualization of the input image, adjusting the contrast of images disrupted the quantitative information because of its nonlinear transforming algorithm. Under certain conditions, adjusting the brightness or the level of images could preserve the quantitative information because of the linear transforming algorithms. It was found that when the minimum and maximum grayscales of a gel image were recognized, using a commercial software package to maximally stretch the level may significantly improve the quality of a gel image without jeopardizing quantitative analysis.     

A thresholding method for automatic cell image segmentation.

An algorithm for automatic segmentation of PAP-stained cell images and its digital implementation is described. First, the image is filtered in order to eliminate the granularily and small objects in the image which may upset the segmentation procedure. In a second step, information on gradient and compactness is extracted from the filtered image and stored in three histograms as functions of the extinction. From these histograms, two extinction thresholds are computed. These thresholds are suitable to separate the nucleus from the cytoplasm, and the cytoplasm from the background in the filtered image. Masks are determined in this way, and finally used to analyse the nucleus and the cytoplasm in the original image.     

Using a multiscale image processing method to characterize the periodic growth patterns on scallop shells

The fine periodic growth patterns on shell surfaces have been widely used for studies in the ecology and evolution of scallops. Modern X‐ray CT scanners and digital cameras can provide high‐resolution image data that contain abundant information such as the shell formation rate, ontogenetic age, and life span of shellfish organisms. We introduced a novel multiscale image processing method based on matched filters with Gaussian kernels and partial differential equation (PDE) multiscale hierarchical decomposition to segment the small tubular and periodic structures in scallop shell images. The periodic patterns of structures (consisting of bifurcation points, crossover points of the rings and ribs, and the connected lines) could be found by our Space‐based Depth‐First Search (SDFS) algorithm. We created a MATLAB package to implement our method of periodic pattern extraction and pattern matching on the CT and digital scallop images available in this study. The results confirmed the hypothesis that the shell cyclic structure patterns encompass genetically specific information that can be used as an effective invariable biomarker for biological individual recognition. The package is available with a quick‐start guide and includes three examples: http://mgb.ouc.edu.cn/novegene/html/code.php .     

Automated measurements on cell nuclei in tissue sections. Validation procedures

A methodology was developed for fully automated measurements of nuclear features in Feulgen-stained tissue sections by means of videomicroscopy and image analysis. Segmentation is performed within one minute on 512 X 512 optical density (OD) images covering about 75 nuclei, resulting in a graphic contour overlay. The corresponding image subset is scanned by an object data extraction program, producing the raw figures for statistical interpretation. The segmentation software was evaluated by three tests, involving comparison with manual delineation and assessment of the influence of OD. Two case studies (ACTH-stimulated adrenal cortex and pancreatic carcinoma) illustrate the biologic accuracy and medical significance of the described methodology.     

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.     

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.     

Development of a universal interface for the exchange of medical image data using magneto-optical media]

Digital images generated by medical imaging form the basis for radiological diagnosis and surgical planning. Despite the advent of the DICOM 3.0 standard for medical image communication, widespread application of the existing information is often limited by incompatibility of the data formatting used by different equipment generations, and the manufacturer-specific standards employed. An exchange interface based on magneto optical discs has been developed to retrieve and present medical image data regardless of the technological hardware and the specific formats used. Specially adapted routines to retrieve the data first had to be developed. A modular program structure was used to allow flexibility in the implementation of further routines and other exchange media. Over 20,000 CT and MRI images including header information obtained from different General Electric and Siemens scanners were extracted successfully from MO discs. The image data were used for follow up and surgical planning and were transferred to a PAC-server. The interface proved reliable and easy to use. Support for further proprietary formats is currently being developed. The present exchange interface permits reliable retrieval of digital images for diagnostic and surgical planning purposes, regardless of the hardware generation and manufacturer-specific formats.     

An implementation of matrix–matrix multiplication on the Intel KNL processor with AVX-512

The second generation Intel Xeon Phi processor codenamed Knights Landing (KNL) have recently emerged with 2D tile mesh architecture and the Intel AVX-512 instructions. However, it is very difficult for general users to get the maximum performance from the new architecture since they are not familiar with optimal cache reuse, efficient vectorization, and assembly language. In this paper, we illustrate several developing strategies to achieve good performance with C programming language by carrying out general matrix–matrix multiplications and without the use of assembly language. Our implementation of matrix–matrix multiplication is based on blocked matrix multiplication as an optimization technique that improves data reuse. We use data prefetching, loop unrolling, and the Intel AVX-512 to optimize the blocked matrix multiplications. When we use a single core of the KNL, our implementation achieves up to 98% of SGEMM and 99% of DGEMM using the Intel MKL, which is the current state-of-the-art library. Our implementation of the parallel DGEMM using all 68 cores of the KNL achieves up to 90% of DGEMM using the Intel MKL.     

XMIPP: a new generation of an open-source image processing package for electron microscopy

X-windows based microscopy image processing package (Xmipp) is a specialized suit of image processing programs, primarily aimed at obtaining the 3D reconstruction of biological specimens from large sets of projection images acquired by transmission electron microscopy. This public-domain software package was introduced to the electron microscopy field eight years ago, and since then it has changed drastically. New methodologies for the analysis of single-particle projection images have been added to classification, contrast transfer function correction, angular assignment, 3D reconstruction, reconstruction of crystals, etc. In addition, the package has been extended with functionalities for 2D crystal and electron tomography data. Furthermore, its current implementation in C++, with a highly modular design of well-documented data structures and functions, offers a convenient environment for the development of novel algorithms. In this paper, we present a general overview of a new generation of Xmipp that has been re-engineered to maximize flexibility and modularity, potentially facilitating its integration in future standardization efforts in the field. Moreover, by focusing on those developments that distinguish Xmipp from other packages available, we illustrate its added value to the electron microscopy community.     

Software package for automatic microarray image analysis (MAIA)

Although various software solutions are currently available for microarray image analysis, one would still expect to develop algorithms ensuring higher level of intelligence and robustness. We present a fully functional software package for automatic processing of the two-color microarray images including spot localization, quantification and quality control. The developed algorithms aim at making ratio estimates more resistant to array contamination and offer automatic tools to evaluate spot quality. Availability: A demo version of the software can be downloaded from http://bioinfo.curie.fr/projects/maia. A full version is freely available to non-commercial users upon request from the authors.     

Computer-aided microtomography with true 3-D display in electron microscopy

A novel research system has been designed to permit three-dimensional (3-D) viewing of high resolution image data from transmission electron microscopy (TEM) and scanning electron microscopy (SEM). The system consists of front-end primary data acquisition devices, such as TEM and SEM machines, which are equipped with computer-controlled specimen tilt stages. The output from these machines is in analogue form, where a video camera attached to the TEM provides the sequential analogue image output while the SEM direct video output is utilized. A 10 MHz digitizer transforms the video image to a digital array of 512 X 512 pixel units of 8 bits deep-stored in a frame buffer. Digital images from multiple projections are reconstructed into 3-D image boxes in a dedicated computer. Attached to the computer is a powerful true 3-D display device which has hardware for graphic manipulations including tilt and rotate on any axis and for probing the image with a 3-D cursor. Data editing and automatic contouring functions are used to enhance areas of interest, and specialized software is available for measurement of numbers, distances, areas, and volumes. With proper archiving of reconstructed image sequences, a dynamic 3-D presentation is possible. The microtomography system is highly versatile and can process image data on-line or from remote sites from which data records would typically be transported on computer tape, video tape, or floppy disk.     

Adaptive color basis transformation. An aid in image segmentation

Multispectral images of stained cells enable the use of color differences to segment and/or to discriminate between image components, such as cell types and cellular subcomponents. When the spectral characteristics of the image components do not change over the area of a slide or from slide to slide, one can create a constant weighted linear combination of spectral images to generate one-dimensional or two-dimensional images that have the desired contrast between the image components that must be discriminated. However, when the spectral characteristics are not constant, i.e., when they vary from image to image, a constant weighted linear combination cannot be employed; instead, an appropriate solution must be found for each selected image. This is usually a time-consuming, manual procedure that cannot be employed in a fully automated process of discriminating and segmenting stained cells. This paper describes an algorithm that uses principal components decomposition basis vectors to generate a nonstatic weighted linear combination of color images that can be used by an automated system. This algorithm relies on a semiconstant relationship between the areas (sizes) of the image components that are to be discriminated and/or segmented. The technique has been successfully applied as an aid in the segmentation of images of stained cervical smears; the images were acquired with a three-chip CCD camera that generates three broad-band color images.