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.     

Mapping Diffusion in a Living Cell via the Phasor Approach

Diffusion of a fluorescent protein within a cell has been measured using either fluctuation-based techniques (fluorescence correlation spectroscopy (FCS) or raster-scan image correlation spectroscopy) or particle tracking. However, none of these methods enables us to measure the diffusion of the fluorescent particle at each pixel of the image. Measurement using conventional single-point FCS at every individual pixel results in continuous long exposure of the cell to the laser and eventual bleaching of the sample. To overcome this limitation, we have developed what we believe to be a new method of scanning with simultaneous construction of a fluorescent image of the cell. In this believed new method of modified raster scanning, as it acquires the image, the laser scans each individual line multiple times before moving to the next line. This continues until the entire area is scanned. This is different from the original raster-scan image correlation spectroscopy approach, where data are acquired by scanning each frame once and then scanning the image multiple times. The total time of data acquisition needed for this method is much shorter than the time required for traditional FCS analysis at each pixel. However, at a single pixel, the acquired intensity time sequence is short; requiring nonconventional analysis of the correlation function to extract information about the diffusion. These correlation data have been analyzed using the phasor approach, a fit-free method that was originally developed for analysis of FLIM images. Analysis using this method results in an estimation of the average diffusion coefficient of the fluorescent species at each pixel of an image, and thus, a detailed diffusion map of the cell can be created.     

Interactive image analysis system to determine the motility and velocity of cyanobacterial filaments

An interactive image analysis system has been developed to analyse and quantify the percentage of motile filaments and the individual linear velocities of organisms. The technique is based on the "difference" image between two digitized images taken from a time-lapse video recording 80 s apart which is overlaid on the first image. The bright lines in the difference image represent the paths along which the filaments have moved and are measured using a crosshair cursor controlled by the mouse. Even short exposure to solar ultraviolet radiation strongly impairs the motility of the gliding cyanobacterium Phormidium uncinatum, while its velocity is not likewise affected. These effects are not due to either type I (free radical formation) or type II (singlet oxygen production) photodynamic reactions, since specific quenchers and scavengers, indicative of these reactions, failed to be effective.     

Quantitative immunohistochemistry by measuring cumulative signal strength accurately measures receptor number.

We previously demonstrated that quantitative immunohistochemistry (Q-IHC) performed by measuring the cumulative signal strength of the digital file encoding an image can be used to determine the absolute amount of chromogen present per pixel. We now show that Q-IHC so performed can be used to accurately determine the amount of peptide hormone receptor of interest in archived tissues. To do this we transfected Balb 3T3 fibroblasts with the cDNA encoding the human receptor for gastrin-releasing peptide (GRP), and selected six cell lines stably expressing between 10(2) and 10(6) receptors/cell. These cell lines were fixed in formalin, embedded in paraffin, and treated with antipeptide antibodies against the GRP receptor, followed by DAB chromogen to identify bound antibody. Images were acquired using a 4.9 million pixel digital scanning 24-bit RGB camera, saved in TIFF format, and used for subsequent analysis. Q-IHC was performed after digitally dissecting out the relevant portion of the image for analysis, and processing using a program written in C (available at http://www.uic.edu/com/dom/gastro/Freedownloads.html). Under the conditions defined here, chromogen quantity as determined by Q-IHC tightly correlated with GRP receptor number (r(2)=0.867) in these cell lines. Using the conversion factor identified as a result of these studies, we then determined GRP receptor number on eight randomly selected, archived human colon cancers. Overall GRP receptor expression in colon cancer depended on the degree to which cells within any particular tumor were differentiated, with well-differentiated cells expressing the greatest numbers of receptors (approximately 55,000 +/- 10,000 sites/cell). These studies indicate that Q-IHC can be used to determine receptor quantity in archived tissues and other samples of limited quantity.     

A program system for interactive measurements on digitized cell images.

Using a high precision image scanner and a PDP-8/F minicomputer, we have developed a program system for interactive measurements on microscopic images. By giving simple keyboard commands, the operator can run the image scanner and manipulate the digitized images. The interface between the operator and the microscope-computer system is a Tektronix 4010 graphic terminal. The system allows objects to be isolated and parameters to be calculated from each object, e.g., parameters characterizing shape of the object, irregularity in light transmission over the object, area, integrated light transmission, etc. Objects are isolated and parameters are calculated under complete operator control using interactive computer graphics technique. Calculated parameters may be stored in dedicated data records, which are stored in files for later statistical analysis. The system also includes a statistical evaluation part. Technically, the system consists of a command scanner, which translates commands into internal representation, a parser, which checks the syntax of the commands, and an interpreter, which executes the commands. The system is designed so that new commands can be added easily.     

植被叶面积指数遥感反演的尺度效应及空间变异性

遥感作为宏观生态学研究中数据获取的一种便捷手段,有助于把握较大尺度内生态学现象的特征.应用遥感数据反演LAI时,由于像元的异质性,不同尺度遥感数据之间的转换是遥感发展的一个重要问题.以河北省黄骅市为研究区,在利用TM和MODIS遥感数据对芦苇LAI反演误差产生原因进行分析的基础上,利用半变异函数对像元空间异质性进行了定量描述.发现NDVI算法的非线性带给LAI尺度转换的误差很小,而LAI的空间异质性则是引起LAI尺度效应的根本原因.并且当像元内空间异质性很大时半变异函数的基台值比纯像元要大得多,空间自相关的程度是引起LAI尺度转换误差的主要原因;反之,像元内空间异质性不大时,随机误差是引起LAI尺度转换误差的主要原因.当像元为纯像元时,由像元异质性引起的反演误差基本可以忽略.此外,研究区芦苇的空间相关有效尺度约为360m,超过此距离空间相关性则不复存在.     

Blood velocity measurement in human conjunctival vessels

The bulbar conjunctiva is one of the few areas in which blood flow in the peripheral vasculature can be directly and noninvasively observed in the human. Although extensive literature exists describing morphological changes which correlate with a variety of systemic diseases in this vasculature, little quantitative data is available on hemodynamics in either normal or abnormal states. The hemodynamic data available are primarily subjective assessments of "low flow." Approaches to place the subjective assessment on more quantitative grounds have usually been based on photographic techniques that have intrinsic inadequacies. The objective of the work reported here was to develop a system capable of providing sequential blood velocity data potentially useful for providing quantitative information on blood flow and its change in the microvessels of the human conjunctiva. The method that has evolved uses a standard Zeiss slit-lamp to image a subject's conjunctival vessels by using a 1-inch Newvicon TV camera with an electronic magnification of 2x. The video image is simultaneously recorded on a video tape recorder (VTR) to an overall system magnification of approximately 4 microm/raster line. The data acquisition phase requires approximately 5 minutes of patient time, whereas the actual determination of blood velocity in individual vessels is done offline through a modification of the dual-slit videodensimetric method. Two independently controllable video cursors are placed axially over the vessel image with the VTR in the still-frame mode. For each consecutive video field, the position of two reference points on the vessel and the position of each cursor relative to these and to each other are encoded into a computer to track the moving image caused by normal eye movement. The computer then determines new cursor coordinates to ensure a constant position within the vessel. The electrical signals obtained for each cursor site and for each video field are cross-correlated to yield the average blood velocity over the sampled time interval. The system has been calibrated in vitro from 0.2 to 2.5 mm/sec, evaluated in experimental animals, and used to measure blood velocity (0.3 to 1.5 mm/sec) in human conjunctival venules with diameters ranging from 20 to 50 microm. At this writing, blood velocity has been recorded during a period of about 3 months in the same vessel of several postmyocardial infarction patients. Thus, the method appears suitable for determining sequential changes in small vessel blood flow in patients over extended periods of time.     

Population estimation of human embryonic stem cell cultures

Traditionally, the population of human embryonic stem cell (hESC) culture is estimated through haemacytometer counts, which include harvesting the cells and manually analyzing a fraction of an entire population. Obviously, through this highly invasive method, it is not possible to preserve any spatial information on the cell population. The goal of this study is to identify a fast and consistent method for in situ automated hESC population estimation to quantitatively estimate the cell growth. Therefore, cell cultures were fixed, stained, and their nuclei imaged through high‐resolution microscopy, and the images were processed with different image analysis techniques. The proposed method first identifies signal and background by computing an image specific threshold for image segmentation. By applying a morphological operator (watershed), we split most physically overlapping nuclei, leading to a pixel area distribution of isolated signal areas on the image. On the basis of this distribution, we derive a nucleus area model, describing the distribution of the area of cell debris, single nuclei, and small groups of connected nuclei. Through the model, we can give a quantitative estimation of the population. The focus of this study is on low‐density human embryonic stem cell populations; hence cultures were measured at days 2–3 after seeding. Compared with manual cell counts, the automatic method achieved higher accuracy with <6% error. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Hypusinated EIF5A as a feasible drug target for Advanced Medicinal Therapies in the treatment of pathogenic parasites and therapy-resistant tumors

Cancer drug resistance, in particular in advanced stages such as metastasis and invasion is an emerging problem. Moreover, drug resistance of parasites causing poverty-related diseases is an enormous, global challenge for drug development in the future. To circumvent this problem of increasing resistance, the development of either novel small compounds or Advanced Medicinal Therapies have to be fostered. Polyamines have many fundamental cellular functions like DNA stabilization, protein translation, ion channel regulation, autophagy, apoptosis and mostly important, cell proliferation. Consequently, many antiproliferative drugs can be commonly administered either in cancer therapy or for the treatment of pathogenic parasites. Most important for cell proliferation is the triamine spermidine, since it is an important substrate in the biosynthesis of the posttranslational modification hypusine in eukaryotic initiation factor 5A (EIF5A). To date, no small compound has been identified that directly inhibits the precursor protein EIF5A. Moreover, only a few small molecule inhibitors of the two biosynthetic enzymes, i.e. deoxyhypusine synthase (DHS) and deoxyhypusine hydroxylase (DOHH) have been functionally characterized. However, it is evident that only some of the compounds have been applied in translational approaches, i.e. in murine models to analyze the function of this modified protein in cell proliferation. In recent years, the pharmaceutical industry shifted from small molecules beyond traditional pharmacology to new tools and methods to treat disorders involving signaling deregulation. In this review, we evaluate translational approaches on inhibition of EIF5A hypusination in pathogenic parasites and therapy-resistant tumors and discuss its feasibility for an application in Advanced Medicinal Therapies.

     

Computer‐automated bird detection and counts in high‐resolution aerial images: a review

Bird surveys conducted using aerial images can be more accurate than those using airborne observers, but can also be more time‐consuming if images must be analyzed manually. Recent advances in digital cameras and image‐analysis software offer unprecedented potential for computer‐automated bird detection and counts in high‐resolution aerial images. We review the literature on this subject and provide an overview of the main image‐analysis techniques. Birds that contrast sharply with image backgrounds (e.g., bright birds on dark ground) are generally the most amenable to automated detection, in some cases requiring only basic image‐analysis software. However, the sophisticated analysis capabilities of modern object‐based image analysis software provide ways to detect birds in more challenging situations based on a variety of attributes including color, size, shape, texture, and spatial context. Some techniques developed to detect mammals may also be applicable to birds, although the prevalent use of aerial thermal‐infrared images for detecting large mammals is of limited applicability to birds because of the low pixel resolution of thermal cameras and the smaller size of birds. However, the increasingly high resolution of true‐color cameras and availability of small unmanned aircraft systems (drones) that can fly at very low altitude now make it feasible to detect even small shorebirds in aerial images. Continued advances in camera and drone technology, in combination with increasingly sophisticated image analysis software, now make it possible for investigators involved in monitoring bird populations to save time and resources by increasing their use of automated bird detection and counts in aerial images. We recommend close collaboration between wildlife‐monitoring practitioners and experts in the fields of remote sensing and computer science to help generate relevant, accessible, and readily applicable computer‐automated aerial photographic census techniques.     

Protein arrangement factor: a new photosynthetic parameter characterizing the organization of thylakoid membrane proteins

A proper spatial distribution of photosynthetic pigment‐protein complexes – PPCs (photosystems, light‐harvesting antennas) is crucial for photosynthesis. In plants, photosystems I and II (PSI and PSII) are heterogeneously distributed between granal and stromal thylakoids. Here we have described similar heterogeneity in the PSI, PSII and phycobilisomes (PBSs) distribution in cyanobacteria thylakoids into microdomains by applying a new image processing method suitable for the Synechocystis sp. PCC6803 strain with yellow fluorescent protein‐tagged PSI. The new image processing method is able to analyze the fluorescence ratios of PPCs on a single‐cell level, pixel per pixel. Each cell pixel is plotted in CIE1931 color space by forming a pixel‐color distribution of the cell. The most common position in CIE1931 is then defined as protein arrangement (PA) factor with xy coordinates. The PA‐factor represents the most abundant fluorescence ratio of PSI/PSII/PBS, the ‘mode color’ of studied cell. We proved that a shift of the PA‐factor from the center of the cell‐pixel distribution (the ‘median’ cell color) is an indicator of the presence of special subcellular microdomain(s) with a unique PSI/PSII/PBS fluorescence ratio in comparison to other parts of the cell. Furthermore, during a 6‐h high‐light (HL) treatment, ‘median’ and ‘mode’ color (PA‐factor) of the cell changed similarly on the population level, indicating that such microdomains with unique PSI/PSII/PBS fluorescence were not formed during HL (i.e. fluorescence changed equally in the whole cell). However, the PA‐factor was very sensitive in characterizing the fluorescence ratios of PSI/PSII/PBS in cyanobacterial cells during HL by depicting a 4‐phase acclimation to HL, and their physiological interpretation has been discussed.     

Tinkerbell—A Tool for Interactive Segmentation of 3D Data

A software system for interactive manipulation of three-dimensional data has been developed, based on the Open Inventor tool kit. The primary use of this software system is in the segmentation of tomographic reconstructions of subcellular structures. To this end, the reconstruction is represented by volume rendering and displayed in stereo. A three-dimensional cursor with adjustable shape and size is used to define and isolate regions of interest inside the volume, based on the user's expert knowledge. Once isolated, the region of interest can be conveniently analyzed and displayed.     

"Clock-scan" protocol for image analysis

Comparative analysis of extra- and intracellular distributions of protein markers in immunohistochemical and immunofluorescent studies relies on techniques of image analysis. Line or region of interest pixel intensity scans are methods routinely used. However, although having good spatial resolution, linear pixel intensity scans fail to produce integral image of the cellular distribution of the label. On the other hand, the regions of interest scans have good integrative capacity but low spatial resolution. In this work, we describe a "clock-scan" protocol that, when applied to convex objects (such as neuronal cell bodies and the majority of cells in culture), combines advantages and circumnavigates limitations of the above-mentioned techniques. The protocol 1) collects multiple radial pixel intensity profiles scanned from the cell center to the periphery, 2) scales these profiles according to the cell radius measured in the direction of the scan, and finally, 3) averages these individual profiles into one integral radial pixel intensity profile. Because of scaling, the mean pixel intensity profiles produced by the clock-scan protocol depend on neither the cell size nor, within reasonable limits, the cell shape. This allows direct comparison or, if required, averaging or subtraction of profiles of different cells. We have successfully tested the clock-scan protocol in experiments with immunostained dorsal root ganglion neurons. In addition, the protocol seems to be equally applicable for studies in a variety of other preparations. techniques; methods; cell biology; histology; immunohistochemistry     

BiNChE: A web tool and library for chemical enrichment analysis based on the ChEBI ontology

Background

Ontology-based enrichment analysis aids in the interpretation and understanding of large-scale biological data. Ontologies are hierarchies of biologically relevant groupings. Using ontology annotations, which link ontology classes to biological entities, enrichment analysis methods assess whether there is a significant over or under representation of entities for ontology classes. While many tools exist that run enrichment analysis for protein sets annotated with the Gene Ontology, there are only a few that can be used for small molecules enrichment analysis.

Results

We describe BiNChE, an enrichment analysis tool for small molecules based on the ChEBI Ontology. BiNChE displays an interactive graph that can be exported as a high-resolution image or in network formats. The tool provides plain, weighted and fragment analysis based on either the ChEBI Role Ontology or the ChEBI Structural Ontology.

Conclusions

BiNChE aids in the exploration of large sets of small molecules produced within Metabolomics or other Systems Biology research contexts. The open-source tool provides easy and highly interactive web access to enrichment analysis with the ChEBI ontology tool and is additionally available as a standalone library.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0486-3) contains supplementary material, which is available to authorized users.     

Quantitative echotexture analysis of bovine ovarian follicles

Computer-assisted image analysis was used to evaluate ultrasound images of bovine ovarian follicles. The ovaries of 8 sexually mature heifers were examined daily by transrectal ultrasonography for 2 estrous cycles. Ultrasonographic examinations of the ovaries were then videotaped, and the dominant and subordinate follicles of successive waves were individually identified and monitored. Recorded images of the dominant anovulatory follicle of the first wave (n = 15) and the ovulatory follicle of the last wave (n = 15) of the estrous cycle were subsequently digitized for computer analysis of echotexture (mean pixel value and pixel heterogeneity). Regions of the image spanning the breadth of the follicle wall were selected, and image analysis revealed that mean pixel value of the dominant anovulatory follicle changed over time (P = 0.0005). Mean pixel value decreased (P = 0.0005) dramatically during the early static phase (Days 6 to 8, Day 0 = day of ovulation), increased (P = 0.0005) at the onset of the regressing phase (Day 12), and reached maximal levels (P = 0.0005) on Day 14. Similarly, image echotexture of the ovulatory follicle revealed a time-dependent effect (P = 0.0001) due to a rapid decrease in mean pixel values between 7 and 4 d before ovulation, followed by an increase until the day before ovulation. The echotexture of images of the follicular antrum were also evaluated and with regard to the dominant anovulatory follicle, a time-dependent effect was not detected for mean pixel value (P = 0.62) but was observed for pixel heterogeneity (P = 0.02). In addition, there was a positive correlation between mean pixel value and heterogeneity (r = 0.61, P = 0.0001). Heterogeneity initially decreased (P = 0.02) and remained low until the emergence of the second follicular wave (mean Day 9). Values subsequently increased and became variable during the late static and regressing phases (> Day 9). Mean pixel value of the antrum of the dominant ovulatory follicle increased (P = 0.0001) as the day of ovulation approached. Heterogeneity did not change (P = 0.14), nor was there any correlation between mean pixel value and heterogeneity for the antrum of the ovulatory follicle (r = 0.06, P = 0.49). We concluded that changes in echotexture (mean pixel value and heterogeneity) of bovine ovarian follicles assessed by computer analysis of ultrasound images were temporally related to functional status (i.e., anovulatory versus ovulatory; growing, static or regressing). The results were strongly supportive of the concept that ultrasonographically detected image attributes are a reflection of physiologic status.     

A 3-D model of membrane specializations between human auditory spiral ganglion cells

A three-dimensional model of the cell membrane contact area was made between two large spiral ganglion cells (type 1 cells) from a cell cluster in a normal human cochlea. The freshly fixed cochlea had been removed during skull base surgery, processed, and sectioned for ultrastructural analysis. 400 consecutive serial thin sections were prepared from the apical portion where the nerve cell density is high and cell clusters are numerous. A cell cluster is defined as a conglomerate of two or more nerve cell bodies, surrounded by common Schwann cells. Direct physical contact between ganglion cell membranes (ephapse) was possible, in places where adjacent cells lacked a separating Schwann cell layer (gaps). One such gap was selected, and observed in 57 of 90 consecutive sections. Membrane specializations, observed in 36 sections, were found to be of principally three different types namely: (1) symmetrical, (2) asymmetrical, and (3) asymmetrical subplasmalemmal. The functional properties of these membrane specializations are still unknown. Asymmetrical densities were seen on one or other of the two cell membranes. A graphic model based on serial thin sections was made to illustrate the gap area. Superficially membrane specializations were seen to form small disk-like areas varying in size, the largest measuring 3 × 2 μm. It is speculated whether these unique formations between human spiral ganglion cells, which have not been observed in other species, may constitute interactive electrotonic or ephaptic transmission pathways. These may be in the low-frequency region and may increase plasticity and signal acuity related to the coding of speech.     

Interactive semisupervised learning for microarray analysis

Microarray technology has generated vast amounts of gene expression data with distinct patterns. Based on the premise that genes of correlated functions tend to exhibit similar expression patterns, various machine learning methods have been applied to capture these specific patterns in microarray data. However, the discrepancy between the rich expression profiles and the limited knowledge of gene functions has been a major hurdle to the understanding of cellular networks. To bridge this gap so as to properly comprehend and interpret expression data, we introduce relevance feedback to microarray analysis and propose an interactive learning framework to incorporate the expert knowledge into the decision module. In order to find a good learning method and solve two intrinsic problems in microarray data, high dimensionality and small sample size, we also propose a semisupervised learning algorithm: kernel discriminant-EM (KDEM). This algorithm efficiently utilizes a large set of unlabeled data to compensate for the insufficiency of a small set of labeled data and it extends the linear algorithm in discriminant-EM (DEM) to a kernel algorithm to handle nonlinearly separable data in a lower dimensional space. The relevance feedback technique and KDEM together construct an efficient and effective interactive semisupervised learning framework for microarray analysis. Extensive experiments on the yeast cell cycle regulation data set and Plasmodium falciparum red blood cell cycle data set show the promise of this approach     

Conversion of monocyte chemoattractant protein-1 into a neutrophil attractant by substitution of two amino acids.

The small cytokine monocyte chemoattractant protein-1 has structural similarity to the neutrophil chemoattractant interleukin-8, but each protein is specific in attracting its own target cell. To investigate the structural basis of this cell type specificity, we have developed an Escherichia coli expression system for the monocyte chemoattractant and mutagenized selected amino acid residues to ones found at the corresponding positions of interleukin-8. We find that a double mutation of tyrosine 28 and arginine 30 to leucine and valine, respectively, causes a drastic decrease in chemotactic activity toward monocytes with the appearance of a novel (interleukin-8-like) neutrophil chemotactic activity. Computer graphic analysis predicts that, with the double substitution, a putative receptor binding groove of the monocyte chemoattractant protein would become topographically similar to that of interleukin-8. We therefore postulate that one or both of these amino acid residues are part of the binding contact of these small cytokines and their receptors.