Voxel-guided morphometry ("VGM") and application to stroke

Monitoring of cerebral diseases associated with a change of morphology (e.g., stroke) requires unprecedented accuracy for quantification of its morphological progression for each voxel. The purpose of this paper is to provide a technique [voxel-guided morphometry (VGM)] to quantify macroscopic anatomical differences. VGM consists of four steps: 1) coarse linear alignment by the extended principle axes theory (ePAT) generalized to affine movements; 2) a cross-correlation-based technique using a matrix-norm for fine linear alignment; 3) the applied high-dimensional multiresolution full multigrid method determines the nonlinear deformations, thereby achieving a complete exploitation of information and effective processing. The method measures a gray-value-guided movement of each voxel from source to target. The resulting high-dimensional deformation field is further processed by 4) determination of volume alterations for each voxel. Furthermore, the effect of linear registration errors on final morphometric measurements is discussed and the conditions for a bijective correspondence of voxels assuming small alterations are derived. To illustrate the technique the changing morphology of different subjects suffering from cerebral infarction is presented by using commonly available T1-weighted magnetic resonance volumes. VGM visualizes that ischemic as well as remote regions are affected by stroke.

Statistics of deformations in histology and application to improved alignment with MRI

An exact registration of magnetic resonance images (MRI) with histological sections is impeded by local deformations resulting from histological preparation procedures. Therefore, it is desirable to know the probability density function of spatial deformations in order to estimate optimal global least-square transformation parameters from suitable landmarks. For this reason, the statistics of deformations is investigated. It is shown analytically that the frequency of occurrence of the absolute geometrical differences (deformations) are Rayleigh-Bessel distributed for anisotropic histological preparation procedures and Rayleigh distributed in the case of isotropic procedures. The probabilistic analysis is given in conjunction with an iterative optimization technique in order to ensure that the probability density function is within a threshold required for the application to experimental data. The application of the analytical model is investigated with real data. It is shown with this data that the extent of deformations varies with the size of the histological section. An individual threshold can be selected on the basis of a Rayleigh-function restricting local corrections to small parts of the image. Thus, global misalignment in each section can be avoided, resulting in an improved 3-D reconstruction of the volume, i.e., the transitions from one section to the next are more continuous.

Three-dimensional component labeling of digital confocal microscope images enumerates replication centers in BrdUrd labeled fibroblasts

An algorithm (3Dlabel-1) for labeling three dimensional binary data sets has been developed. Serial optical sections are acquired using a confocal laser scanning microscope. After filtering and thresholding operations, contiguous elements in the three dimensional data sets are identified and labeled. The results are used to calculate the number and size of objects. Additionally, the labeled data are displayed by applying an algorithm (3Ddisp-1) to generate stereo pairs, in which label numbers are color coded and depth is cued by intensity. These procedures have been applied in investigations of the temporal and spatial distribution of replication centers throughout S phase in BrdUrd pulse labeled mouse fibroblasts.

Three-dimensional DNA image cytometry by confocal scanning laser microscopy in thick tissue blocks

A method for the quantification of nuclear DNA in thick tissue blocks by confocal scanning laser microscopy is presented. Tissues were stained en bloc for DNA by chromomycin A3. Three-dimensional images, 60 microns deep, were obtained by stacking up confocal fluorescent images obtained with an MRC-500 (Bio-Rad, Richmond, CA). The effects due to bleaching and attenuation by depth of fluorescence emission were corrected mathematically. The DNA contents were estimated by summing up the detected emission intensities (discretized into pixel gray levels) from each segmented nucleus. Applications to an adult rat liver and to a human in situ carcinoma of theesophagus are shown to demonstrate, respectively, the precision of the method and its potential usefulness in histopathology. Comparisons are made with DNA histograms obtained on the same materials by image cytometry on smears and by flow cytometry. Ploidy peaks obtained with the confocal method, although wider than with other methods, are well separated. Confocal image cytometry offers the invaluable advantage of preserving the tissue architecture and therefore allowing, for instance, the selection of histological regions and the evaluation of the degree of heterogeneity of a tumor.

Probing DNA structure and function with a multi-wavelength fluorescence confocal laser microscope

Three levels of organization in DNA structure in the interphase cell nucleus are assessed by confocal laser scanning microscopy: (i) the conformational state of the double helix; (ii) the distribution of eu- and heterochromatin; and (iii) the localization of replication complexes throughout S phase. Multi-parameter measurements were carried out in each optical section using two laser sources and combined stereoscopic reconstructions were used to assess the co-localization of nuclear components. DNA is highly polymorphic and can adopt a variety of different helical conformations as well as unusual structures (curved, cruciform, multi-stranded). We have assessed by laser scanning microscopy the presence of left-handed Z-DNA in polytene chromosomes of Diptera as well as the spatio-temporal distribution of Z-DNA binding proteins in whole-mount Drosophila embryos and ovaries. We have determined the 3-D distribution of replication sites relative to heterochromatin regions, nucleoli and nuclear membrane by using short pulses of BrdU incorporation in synchronized mouse and human fibroblasts. Replication sites were visualized with a monoclonal anti-BrdU antibody combined with DNA fluorescent staining and antibody labelling of nuclear lamin. The implications of dynamic DNA movement and structural rearrangement to the organization of the nucleus in domains are discussed.