Combined method of whole mount and block-face imaging: Acquisition of 3D data of gene expression pattern from conventional in situ hybridization

Visualization of spatiotemporal expression of a gene of interest is a fundamental technique for analyzing the involvements of genes in organ development. In situ hybridization (ISH) is one of the most popular methods for visualizing gene expression. When conventional ISH is performed on sections or whole-mount specimens, the gene expression pattern is represented in 2-dimensional (2D) microscopic images or in the surface view of the specimen. To obtain 3-dimensional (3D) data of gene expression from conventional ISH, the “serial section method” has traditionally been employed. However, this method requires an extensive amount of time and labor because it requires researchers to collect a tremendous number of sections, label all sections by ISH, and image them before 3D reconstruction. Here, we proposed a rapid and low-cost 3D imaging method that can create 3D gene expression patterns from conventional ISH-labeled specimens. Our method consists of a combination of whole-mount ISH and Correlative Microscopy and Blockface imaging (CoMBI). The whole-mount ISH-labeled specimens were sliced using a microtome or cryostat, and all block-faces were imaged and used to reconstruct 3D images by CoMBI. The 3D data acquired using our method showed sufficient quality to analyze the morphology and gene expression patterns in the developing mouse heart. In addition, 2D microscopic images of the sections can be obtained when needed. Correlating 2D microscopic images and 3D data can help annotate gene expression patterns and understand the anatomy of developing organs. These results indicated that our method can be useful in the field of developmental biology.     

Imaging of surface cell antigens on the tumor sections of lymph nodes using fluorescence quantum dots

The usefulness of quantum dots for the immunofluorescent detection of surface antigens on the lymphoid cells has been studied. To optimize quantum dots detection we have upgraded fluorescent microscope that allows obtaining multiple images from different quantum dots from one section. Specimens stained with quantum dots remained stable over two weeks and practically did not bleach under mercury lamp illumination during tens of minutes. Direct conjugates of primary mouse monoclonal antibodies with quantum dots demonstrated high specificity and sufficient sensitivity in the case of double staining on the frozen sections. Because of the high stability of quantum dots' fluorescence, this method allows to analyze antigen coexpression on the lymphoid tissue sections for diagnostic purposes. The spillover of fluorescent signals from quantum dots into adjacent fluorescent channels, with maxima differing by 40 nm, did not exceed 8%, which makes the spectral compensation is practically unnecessary.     

基于计算机三维图象技术的失语症病灶空间定位法

首次把计算机三维重建方法应用于失语症的研究中,主要有三方面的工作:(1)建立了一套精细程度较高的标准CT脑图,用三维重建方法建立了标准立体头颅,并用伪彩色显示不同的脑结构和语言区.(2)提出标准化应在三维空间内进行的观点,改进的标准化方法充分利用了CT所能提供的关于脑结构的信息,从而使病灶在每层标准CT脑图上的定位更加准确.(3)对两类临床表现不同但CT显示病灶位置相近的失语症病人共47例进行了研究.通过对标准化之后的病灶的统计处理,得到病灶的集中部位,并对其进行三维重建,在标准立体头颅中显示其空间位置的差别.     

A Reference-Free Method for Brightness Compensation and Contrast Enhancement of Micrographs of Serial Sections

Three-dimensional (3D) reconstruction of an organ or tissue from a stack of histologic serial sections provides valuable morphological information. The procedure includes section preparation of the organ or tissue, micrographs acquisition, image registration, 3D reconstruction, and visualization. However, the brightness and contrast through the image stack may not be consistent due to imperfections in the staining procedure, which may cause difficulties in micro-structure identification using virtual sections, region segmentation, automatic target tracing, etc. In the present study, a reference-free method, Sequential Histogram Fitting Algorithm (SHFA), is therefore developed for adjusting the severe and irregular variance of brightness and contrast within the image stack. To apply the SHFA, the gray value histograms of individual images are first calculated over the entire image stack and a set of landmark gray values are chosen. Then the histograms are transformed so that there are no abrupt changes in progressing through the stack. Finally, the pixel gray values of the original images are transformed into the desired ones based on the relationship between the original and the transformed histograms. The SHFA is tested on an image stacks from mouse kidney sections stained with toluidine blue, and captured by a slide scanner. As results, the images through the entire stack reveal homogenous brightness and consistent contrast. In addition, subtle color differences in the tissue are well preserved so that the morphological details can be recognized, even in virtual sections. In conclusion, compared with the existing histogram-based methods, the present study provides a practical method suitable for compensating brightness, and improving contrast of images derived from a large number of serial sections of biological organ.     

植物组织石蜡切片的扫描电镜观察方法研究

石蜡切片的扫描电镜观察法有其独到之处:集光镜和扫捕电镜特长于一体,在大量的石蜡切片光镜观察的基础上,挑选具有研究线索的切片,采用此法转移到扫描电镜下作高分辩研究,既可普查切片全貌,又可处得切片中亚微结构的三维图像,这对结构的准确分辩十分有利,且便于作连续切片观察。本文简要介绍这一实验技术。     

Film tomography as a tool for three-dimensional image construction and gene expression studies

In order to observe three-dimensional (3D) expression patterns of genes in whole animals, whole organs, or whole tissues, in situ hybridization (ISH) of many sections must be carried out and then used to construct a 3D image. For this purpose, we have developed an automatic microtome to prepare tissue sections with an adhesive film. We used commercially available film suitable for sectioning and ISH. We constructed a microtome and, after adherence of the film to a paraffin-embedded tissue block, cut the block with a blade to prepare sections on film. Then, the sections-on-film were automatically set in a plastic frame that was the same size as a conventional glass slide. With this automatic microtome, tissue sections can be made for ISH or immunohistochemistry in addition to conventional hematoxylin and eosin staining without specific training. We demonstrate that we can construct 3D images of gene expression patterns obtained by ISH on sections prepared with this automatic microtome. We have designated this method as 'Film Tomography (FITO)'.     

Invertebrate myosin filament: Parallel subfilament arrangement in the wall of solid filaments from the honeybee, Apis mellifica

Transverse serial sections (100-140 nm thick) of solid myosin filaments of the honeybee, Apis mellifica, were photographed in a JEM-200 electron microscope at 200 kV. The images were digitized and computer processed by rotational filtering. 87% of the myosin filaments showed 6-fold symmetry in their power spectra, confirming the results of earlier works (Beinbrech et al., 1988, 1991). To determine if the subfilaments were arranged parallel to the filament backbone, two methods were used. First, the three images of each myosin filament in the three serial sections were superimposed. 85% of the resulting images showed a strong peak for 6-fold symmetry and the averaged images showed 6 pairs of subfilaments, which gives evidence for parallel arrangement of the subfilaments relative to the filament axis. This result was confirmed by the second method in which a 3-dimensional reconstruction was made. An average image was made from the images of the same 17 myosin filaments from each of the three sections. The data for the 3-dimensional reconstruction were collected by tracing the outlines of the structures in the three successive sections. The resulting stereo image shows a parallel arrangement of the subfilaments.     

A rapid procedure for preparing fluorescein-labeled specific antibodies from whole antiserum: its use in analyzing cytoskeletal architecture

A rapid method for the direct conjugation of affinity-purified antibodies with fluorescein (termed DCAPA) is described. This procedure involves the immobilization of antibodies as antigen-antibody complexes on nitrocellulose blots, and subsequently the bound antibodies are reacted with fluorescein isothiocyanate. An enriched sample of smooth muscle tropomysin transferred to nitrocellulose paper by the Western blotting procedure has been used as the affinity medium for purification of specific tropomyosin antibody from whole rabbit antiserum. Direct conjugation of the antibody with fluorescein was carried out following the binding of antibody to antigen. Direct conjugation and affinity purification of antibodies directed against tropomyosin was accomplished in 2-3 d using an enriched tropomyosin sample and whole antiserum directed against tropomyosin. The immunofluorescence images obtained with this procedure exhibit distinct advantages with regard to background fluorescence and overall specificity of antibody binding. The usefulness of this direct conjugation method in various experimental protocols is discussed.     

Characterization of dynamic three-dimensional strain fields in the canine radius

This note describes a method to approximate the 3-D mechanical environment of a long bone during a normal daily activity. Our specific goal was to characterize the temporal and spatial strain distributions in the mid-shaft region of the canine radius during gait. Direct measurement of strains along the entire surface of in vivo bone is not feasible, so we employed a combination of experimental measurements and numerical interpolation techniques to approximate the time-varying longitudinal strain distribution. Using standard in vivo strain gauging techniques, we measured dynamic strains at nine locations (three locations on each of three cross sections, data pooled from two experimental animals) on the canine radius during trotting gait. These in vivo strain measurements were then used to approximate the time course of the strain field for the entire radius mid-shaft region using a 3-D numerical interpolation scheme using finite element basis functions. Despite limitations in the present implementation of the method, the results show that there are considerable time-dependent variations in the strain distribution occurring at different transverse sections along the length of the diaphysis with substantial anteroposterior bending and rotation of neutral axis locations during the gait cycle.     

生物组织显微结构三维重建的灰度阴影立体图对显示技术

本文描述了一种新的显示三维重建模型的方法—灰度阴影立体图对方法(shading-stereo-pair method).该方法根据连续切片三维重建的灰度阴影法和立体图对法的显示原理,导出了生成立体图对的视差公式.在灰度阴影法三维重建过程中,根据各切片所处的深度和其本身的厚度,按视差公式计算出它们在图对上的位移量并进行水平方向的移动,经过对各切片的叠加和重组,最后生成一幅具有视差信息的灰度阴影立体图对.在体视仪下观察,即可看到重建模型的三维实体图象.最后还讨论了进一步提高图象质量和改善观察效果所必须采取的措施.     

Analysis by Confocal Microscopy of the Structure of Cambium in the Hardwood Kalopanax pictus

An understanding of the morphology and the developmental changesin the shapes and dimensions of cambial cells requires three-dimensional(3-D) analysis of thick slices of tissue. We devised a simpleprotocol using confocal laser scanning microscopy (CLSM), withsafranin and acridine orange as fluorescent dyes and glycerolas the clearing and mounting medium, to examine the 3-D structureof the dormant cambium in Kalopanax pictus, a ring-porous hardwood.Optical sections and high contrast images provided clear informationabout the shapes and nuclear status of cambial cells, whichhave previously been difficult to determine using conventionalmicroscopy. The axially-oriented cambial cells were found tovary in shape, in particular around the rays, and were not alwaystypically fusiform. We evaluated the reliability of our methodby comparing results with those of a parallel study of the samematerial by standard analysis of serial sections of epoxy-embeddedspecimens. The images of optical sections obtained by CLSM wereof high quality and similar to images obtained by conventionallight microscopy of semi-thin mechanical sections. Use of theconfocal microscope provided a quick and easy method for visualizationof the structure of the cambium in thick hand-cut sections andfor studies of the developmental changes in cells from the cambiumto the xylem. Copyright 2000 Annals of Botany Company Confocal laser scanning microscopy, Kalopanax pictus, three-dimensional reconstruction, vascular cambium     

Structure of activated sludge floes

Relatively large activated sludge floes (larger than about 100 mum) were stabilized, using a histological tissue specimen preparation procedure, and then were sliced into sections of 3 to 6 mum thick. The study of these sections, after staining, revealed the internal structure of the activated sludge floes. No uniformity of this structure was found. The distribution of microorganisms and of extracellular polymers (EPs) in the floes varied randomly on the plane of the sections and along the dimension perpendicular to the plane, leaving large water channels and reservoirs in some of the floes. The lack of a characteristic size for the water gaps in the floes and a general self-similar appearance of the sections suggested that the activated sludge floes might be characterized by the fractal concept within a certain size limit. Direct observation of the interior of the floes indicated an abundant presence of extracellular polymers (EPs) in amorphous forms, surrounding microorganisms in most of the floes.     

微波快速免疫荧光组化染色方法的研究

本文应用微波辐射方法加速免疫荧光组化染色(间接和直接法),分别定位15种不同组织抗原,并应用连续切片同时用两种不同的孵育方法即微波辐射和常规孵育方法进行比较。结果证明,经微波辐射后免疫荧光组化染色时间大大缩短,背景染色明显好于常规法,阳性率和阳性强度与常规法基本一致。     

A quantitative method to determine the orientation of collagen fibers in the dermis.

We have developed a quantitative microscopic method to determine changes in the orientation of collagen fibers in the dermis resulting from mechanical stress. The method is based on the use of picrosirius red-stained cryostat sections of piglet skin in which collagen fibers reflect light strongly when epipolarization microscopy is used. Digital images of sections were converted into binary images that were analyzed quantitatively on the basis of the length of the collagen fibers in the plane of the section as a measure for the orientation of the fibers. The length of the fibers was expressed in pixels and the mean length of the 10 longest fibers in the image was taken as the parameter for the orientation of the fibers. To test the procedure in an experimental setting, we used skin after 0 and 30 min of skin stretching. The orientation of the fibers in sections of control skin differed significantly from the orientation of fibers in sections of skin that was stretched mechanically for 30 min [76 +/- 15 (n=5) vs 132 +/- 36 (n=5)]. The method described here is a relatively simple way to determine (changes in) the orientation of individual collagen fibers in connective tissue and can also be applied for analysis of the orientation of any other structural element in tissues so long as a representative binary image can be created.     

Analysis of CD36 expression on human monocytic cells and atherosclerotic tissue sections with quantum dots: investigation by flow cytometry and spectral imaging microscopy

OBJECTIVE: To demonstrate CD36 expression with quantum dots (QDs) 525 and/or 605 on human monocytic U937 cells and atherosclerotic tissue sections by means of flow cytometry (FCM) and/or confocal laser scanning microscopy (CLSM). STUDY DESIGN: U937 cells and tissue sections were analyzed by means of FCM and/or CLSM. FCM was performed, using different ultraviolet (UV) and visible (488/532 nm) excitation modes. In the visible mode, fluorescence intensities of QDs, phycoerythrin (PE) and fluorescein isothiocyanate (FITC) were compared. Three-dimensional (3-D) sequences of images were obtained by spectral analysis in a CLSM and analyzed by the factor analysis of medical image sequences (FAMIS) algorithm, providing factor curves and images. Factor images are the result of the FAMIS image processing method, which differentiates emission spectra from 3D sequences of images. In CLSM analysis, preparations are screened in a UV excitation mode to optimize the possibilities of QDs and have the benefit of 4',6-diamino-2-phenylindole or Hoechst 33342 counterstaining of nuclei. RESULTS: FCM and CLSM revealed CD36 expression by means of QDs 525 and/or 605. Fluorescence intensity of PE and of FITC was higher than that of QDs 525 and of 605. As factor curves and images show the red emission of QDs 605 only, subsequent reliable identification and localization of CD36 was obtained. CONCLUSION: QDs 525 and 605 are useful to analyze antigenic expression. Following FCM, which is well adapted to detect fluorescence emission of QDs in the UV or visible excitation mode, CLSM and subsequent spectral analysis assess more specific characterization of QD fluorescent emissions.     

A comparison of image processing techniques for bird recognition

Bird predation is one of the major concerns for fish culture in open ponds. A novel method for dispersing birds is the use of autonomous vehicles. Image recognition software can improve their efficiency. Several image processing techniques for recognition of birds have been tested. A series of morphological operations were implemented. We divided images into 3 types, Type 1, Type 2, and Type 3, based on the level of difficulty of recognizing birds. Type 1 images were clear; Type 2 images were medium clear, and Type 3 images were unclear. Local thresholding has been implemented using HSV (Hue, Saturation, and Value), GRAY, and RGB (Red, Green, and Blue) color models on all three sections of images and results were tabulated. Template matching using normal correlation and artificial neural networks (ANN) are the other methods that have been developed in this study in addition to image morphology. Template matching produced satisfactory results irrespective of the difficulty level of images, but artificial neural networks produced accuracies of 100, 60, and 50% on Type 1, Type 2, and Type 3 images, respectively. Correct classification rate can be increased by further training. Future research will focus on testing the recognition algorithms in natural or aquacultural settings on autonomous boats. Applications of such techniques to industrial, agricultural, or related areas are additional future possibilities.     

3D reconstruction of dental specimens from 2D histological images and microCT-scans

Direct comparison of experimental and theoretical results in biomechanical studies requires a careful reconstruction of specimen surfaces to achieve a satisfactory congruence for validation. In this paper a semi-automatic approach is described to reconstruct triangular boundary representations from images originating from, either histological sections or microCT-, CT- or MRI-data, respectively. In a user-guided first step, planar 2D contours were extracted for every material of interest, using image segmentation techniques. In a second step, standard 2D triangulation algorithms were used to derive high quality mesh representations of the underlying surfaces. This was accomplished by converting the 2D meshes into 3D meshes by a novel lifting procedure. The meshes can be imported as is into finite element programme packages such as Marc/Mentat or COSMOS/M. Accuracy and feasibility of the algorithm is demonstrated by reconstructing several specimens as examples and comparing simulated results with available measurements performed on the original objects.     

Laser capture microdissection of bacterial cells targeted by fluorescence in situ hybridization

Direct cultivation-independent sequence retrieval of unidentified bacteria from histological tissue sections has been limited by the difficulty of selectively isolating specific bacteria from a complex environment. Here, a new DNA isolation approach is presented for prokaryotic cells. By this method, a potentially pathogenic strain of the genus Brachyspira from formalin-fixed human colonic biopsies were visualized by fluorescence in situ hybridization (FISH) with a 16S rRNA-targeting oligonucleotide probe, followed by laser capture microdissection (LCM) of the targeted cells. Direct 16S rRNA gene PCR was performed from the dissected microcolonies, and the subsequent DNA sequence analysis identified the dissected bacterial cells as belonging to the Brachyspira aalborgi cluster 1. The advantage of this technique is the ability to combine the histological recognition of the specific bacteria within the tissue with molecular analysis of 16S rRNA gene or other genes of interest. This method is widely applicable for the identification of noncultivable bacteria and their gene pool from formalin-fixed paraffin-embedded tissue samples.     

Structure of solid-supported lipid membrane probed by noble metal nanoparticle deposition

Direct deposition of a noble metal layer onto a solid-supported membrane was proposed as an indirect microscopy tool to visually observe different lipid phases that may develop in the lipid membrane. The method relied on the different permeability of the lipid membrane towards the incident atoms during deposition. Liquid state or structural defects such as phase boundaries, step ledges in a multi-lamellar stack, and pores permitted the metal atoms to penetrate and nucleate inside the membrane whereas rigid gel state was relatively impermeable to the incident atoms, thus enabling visualization of liquid phase or structural defects inside the gel state. Based on the proposed method, we demonstrated the phase states resulting from thermotropic transitions of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), dioleoylphosphatidylethanolamine (DOPE)/DPPC mixture, and 1,2-dioleoyl-3-trimethylammonium propane (DOTAP). Although the proposed method does not allow in-situ observation of equilibrium states, the method should be an excellent complementary tool for visualizing the lipid phases as the method can resolve fine structural details (up to tens of nanometer scale) as seen in the DPPC membrane while providing macroscopic images (up to several micrometers).     

Method to classify xylem cell types using cross sectionsof 1-year-old branches in Mediterranean woody species

Measurements of anatomical parameters of wood are of great interest both for eco-physiological purposes and for technological applications. The aim of this paper is to describe a new method for classifying and measuring cell lumen of xylem, analysing cross sections under the light microscope. The proposed method is based on the application of digital image analysis on images of the cross sections of xylem in combination with graphical and statistical methods. The methodology was tested on 1-year-old branches of several woody species, both trees and shrubs, occurring in a Mediterranean natural ecosystem in southern Italy. The development of the procedure was based on statistical comparison between data collected according to four procedures: (a) manual identification and measurement of lumen diameter of conduits on longitudinal sections; (b) manual identification and measurement of lumen diameter of conduits on cross sections; (c) manual identification and measurement of lumen area of conduits on cross sections; and (d) automatic measurement of lumen area of conduits on cross sections. The influence of image resolution and that of the position of the selected area on cell classification and measurements were ascertained. The proposed method was proved to be specific to woody structures and allowed the construction of a model-graph that is species-specific. Interpretation of the model-graphs allows classification and hence measurement of identified cells.