Segmentation of cell nuclei in tissue section analysis

Reverse genetic screen reveals that Il34 facilitates yolk sac macrophage distribution and seeding of the brain

Microglia are brain-resident macrophages, which have specialized functions important in brain development and in disease. They colonize the brain in early embryonic stages, but few factors that drive the migration of yolk sac macrophages (YSMs) into the embryonic brain, or regulate their acquisition of specialized properties, are currently known. Here, we present a CRISPR/Cas9-based in vivo reverse genetic screening pipeline to identify new microglia regulators using zebrafish. Zebrafish larvae are particularly suitable due to their external development, transparency and conserved microglia features. We targeted putative microglia regulators, by Cas9/gRNA complex injections, followed by Neutral-Red-based visualization of microglia. Microglia were quantified automatically in 3-day-old larvae using a software tool we called SpotNGlia. We identified that loss of zebrafish colony-stimulating factor 1 receptor (Csf1r) ligand, Il34, caused reduced microglia numbers. Previous studies on the role of IL34 in microglia development in vivo were ambiguous. Our data, and a concurrent paper, show that, in zebrafish, il34 is required during the earliest seeding of the brain by microglia. Our data also indicate that Il34 is required for YSM distribution to other organs. Disruption of the other Csf1r ligand, Csf1, did not reduce microglia numbers in mutants, whereas overexpression increased the number of microglia. This shows that Csf1 can influence microglia numbers, but might not be essential for the early seeding of the brain. In all, we identified il34 as a modifier of microglia colonization, by affecting distribution of YSMs to target organs, validating our reverse genetic screening pipeline in zebrafish.This article has an associated First Person interview with the joint first authors of the paper.

A survey on histological image analysis-based assessment of three major biological factors influencing radiotherapy: proliferation, hypoxia and vasculature

Image analysis is a rapidly evolving field with growing applications in science and engineering. In cancer research, it has played a key role in advancing techniques of major diagnostic importance, minimising human intervention and providing vital clinical information. Especially in the field of tissue microscopy, the use of computers for the automated analysis of histological sections is becoming increasingly important. This paper presents an overview of various image analysis methodologies and summarises developments in this field, with great emphasis given on the assessment of three major biological factors known to influence the outcome of radiotherapy: proliferation, vasculature and hypoxia. A brief introduction followed by a survey is provided in each of these areas.

Chromatin organization and breast cancer prognosis. Two-dimensional and three-dimensional image analysis

BACKGROUND

The assessment of breast cancer prognosis still relies on clinical staging and histologic grading. Among the different prognostic parameters, attention has been focused on features of chromatin structure. Although data from two-dimensional (2-D) analysis of chromatin structure show significant correlation with the survival, their biologic interpretation remains difficult. In this respect, insights into the spatial organization of chromatin appear important.

METHODS

The authors performed computerized three-dimensional (3-D) reconstructions of Feulgen-stained tumor cell nuclei, correlating the results with those of 2-D image analysis. Forty-nine ductal-invasive carcinomas with 10-18 years follow-up were investigated.

RESULTS

The 2-D analysis demonstrated that along with nuclear size and shape, chromatin features such as marginal concentration of condensed chromatin are of prognostic importance. As 3-D analysis revealed, chromatin changes concern ordered organization and were associated with the increase of spatial entropy.

CONCLUSIONS

The 3-D description of chromatin structure by means of spatial models provides evidence that tumor aggressiveness correlates with events of clustering and randomization. These indicate disturbances of ordered chromatin organization.

Quantitative features of chromatin structure in the prognosis of breast cancer

In prognosis of breast cancer different parameters are in current use. Along with clinical staging the most important parameter appears to be histologic grading. Features of the grading such as nuclear pleomorphism proved to correlate closely with the proliferative activity and aggressiveness of the tumors. Because of difficulties in assessing and classifying the degree of nuclear pleomorphism by usual microscopy, the authors applied methods of digital image analysis. The study is a retrospective analysis of paraffine slides from the primary lesions of 60 breast cancers with 10 to 16 years of follow-up evaluation. Using large sets of different parameters defining nuclear morphology and chromatin structure the authors extracted criteria with prognostic importance. These included nuclear area in micron 2, eccentricity, integral optical density per micron 2, average area of a chromatin region, integral optical density of a chromatin region per micron 2, and the number of central chromatin regions per micron 2. The results demonstrate that the criteria used enable prediction of prognosis with an accuracy of 92%.

Image analysis of Nissl-stained neuronal perikarya in the primary visual cortex of the rat: automatic detection and segmentation of neuronal profiles with nuclei and nucleoli

An image analysing procedure for the morphometric characterization of cortical neurons in Nissl-stained brain sections is described. It consists of the automatic detection of cellular profiles and their compartments: cytoplasm, nucleus and nucleolus. The algorithm was designed to cope with the large morphological spectrum of cortical perikarya (e.g. geometrical properties of perikarya, staining intensities of cell compartments and nucleo-plasmic area-ratio) including pyramidal (Golgi-category I) and non-pyramidal (Golgi-category II) neurons. Clusters of cells were separated and non-neuronal structures (e.g. glia, endothelial cells) as well as tangential, non-nucleolated sections through neuronal perikarya recognized and excluded from further analysis without requiring interactive procedures. The performance of the profile recognition procedure was evaluated using 426 nucleolated and non-nucleolated profiles of different types of neurons in the primary visual cortex of the rat. Nucleolated profiles were recognized as such with a 91% accuracy, non-nucleolated profiles were rejected correctly in 90% of cases. After automatic segmentation and selection of nucleolated neuronal profiles from the microscopic field, a large set of quantitative morphological features including geometrical, densitometrical and textural parameters can be measured using high power light microscopy. This permits quantitative morphometric characterization of different neuronal types. This procedure is the first part of a system for the automatic classification of Nissl-stained cortical neurons.

Quantitative nuclear morphology in the diagnosis of ovarian tumors of low malignant potential (borderline)

Ovarian tumors of low malignant potential or of borderline malignancy are characterized histologically by the association of malignant type of epithelial proliferation with a noninvasive pattern of growth. Because epithelial proliferation relates to features of nuclear morphology and chromatin structure and because of the difficulties to distinguish nuclear atypism seen in borderline malignancy from that in frankly invasive tumors by usual microscopic study, the authors concentrated their studies exclusively on computerized analysis of cell nuclei images. Using specially developed methods of analysis the authors described geometrical, optical, and structural differences among the epithelial and stromal cell nuclei of benign, borderline, and malignant ovarian tumors. The structural differences concern the pattern of chromatin condensation and suggest that the cytokinetic properties of the borderline tumors are intermediate to those of benign and malignant. The results demonstrate that the quantitative evaluations provide objective and reproducible data useful in the differential diagnostic of the borderline malignancy.

Double in situ hybridization in combination with digital image analysis: a new approach to study interphase chromosome topography

Double in situ hybridization with mercurated and biotinylated chromosome specific DNA probes in combination with digital image analysis provides a new approach to compare the distribution of homologous and nonhomologous chromosome targets within individual interphase nuclei. Here we have used two DNA probes representing tandemly repeated sequences specific for the constitutive heterochromatin of the human chromosomes 1 and 15, respectively, and studied the relative arrangements of these chromosome targets in interphase nuclei of human lymphocytes, amniotic fluid cells, and fibroblasts, cultivated in vitro. We have developed a 2D-image analysis approach which allows the rapid evaluation of large numbers of interphase nuclei. Models to test for a random versus nonrandom distribution of chromosome segments are discussed taking into account the three-dimensional origin of the evaluated 2D-distribution. In all three human diploid cell types the measurements of target-target and target-center distances in the 2D-nuclear image revealed that the labeled segments of the two chromosomes 15 were distributed both significantly closer to each other and closer to the center of the nuclear image than the labeled chromosome 1 segments. This result can be explained by the association of nucleolus organizer regions on the short arm of chromosome 15 with nucleoli located more centrally in these nuclei and does not provide evidence for a homologous association per se. In contrast, evaluation of the interphase positioning of the two chromosome 1 segments fits the random expectation in amniotic fluid and fibroblast cells, while in experiments using lymphocytes a slight excess of larger distances between these homologous targets was occasionally observed. 2D-distances between the labeled chromosome 1 and 15 segments showed a large variability in their relative positioning. In conclusion our data do not support the idea of a strict and permanent association of these homologous and nonhomologous targets in the cell types studied so far.

Structural changes in nuclear chromatin in rat pituitary after chronic stress of low intensity

Acute, intense sources of "psychogenic" stress clearly modify the structure and function of the hypophysis, and there are concomitant changes in many peripheral physiological systems. Less dramatic sources of stress yield more equivocal results. An experiment is reported in which nuclear morphology of adenohypophyseal cells from 49 male rats exposed to a chronic, low-intensity stressor was examined both by conventional histological and computer-assisted-image-processing methods. The hypothesis tested was that an unequivocal pattern of morphological changes in the nucleus and nuclear chromatin would be revealed by image processing. Rats were killed after living for a year in a relatively low-stress environment, "crowded" in groups of five animals per cage. The control condition was a minimal stress environment of two rats per cage. Results suggested few signs of pathology from peripheral measures of hypophyseal activity, and direct light microscopic examination of the gland revealed no differences between the two groups. Analysis of computer-enhanced images of the pars distalis nuclei from the adenohypophysis, on the other hand, generated findings that were statistically and biologically significant. Nuclear size increased in the stress condition, the number of chromatin and area occupied by the particles increased, and the position of chromatin shifted toward the periphery of the nucleus. Perhaps more important, optical density analysis indicated that chromatin was less tightly packed in the experimental animals. Implications are that chronic, low-intensity stress modulates nuclear structural changes from a dormant to an active state that portend changes in the peripheral systems influenced by the hypophysis.

Quantitative description of nuclear morphology in assessing resistance of sarcoma 180 to adriamycin

Resistance to adriamycin generally is explained through changes of cell/drug interactions that possibly reflect structural alterations of intracellular targets. One of the main targets of adriamycin is believed to be nuclear chromatin. In order to recognize chromatin alterations, we studied cell nuclei morphology and chromatin structure by means of digital image analysis. The studies were performed in both adriamycin-sensitive and -resistant Sarcoma 180 cell lines which were cultured under growth-stimulated and nonstimulated conditions. Using specially developed methods, we extracted parameters characterizing geometrical, optical, and structural properties of the cell nuclei from light microscopical images. The latter parameters concerned microscopical appearances of condensed chromatin and were described by features of high-optical-density regions. The results demonstrated that the quantitative criteria applied enabled the discrimination of sensitive and resistant cells. The most important parameters are the nuclear size, number, distribution, and optical density of condensed chromatin regions. In addition, the criteria permit recognition of changes related to differences in the growth conditions of the cells. The data of the image analysis suggest that adriamycin resistance in Sarcoma 180 cells is associated with characteristic patterns of cell nuclear morphology which can be described with a sufficient number of appropriate parameters. The advantages of image analysis are evident when these results are compared with the flow cytometric findings. The conclusion is that structural features of nuclear chromatin provide information essential for the assessment of drug resistance.

Image analysis of hepatocyte nuclei in assessing di(2-ethylhexyl)phthalate effects eluding detection by conventional microscopy

The effect of di(2-ethylhexyl)phthalate (DEHP) administered in single intraperitoneal doses of 30, 300 and 3000 mg/kg in Syrian golden hamsters was studied by means of routine pathologic investigations, electron microscopy and image analysis. The morphological evaluations did not show apparent differences between the control and treated animals. Such differences, however, were recognized by using image analysis. They concerned morphology of the hepatocyte nuclei and were defined by quantitative parameters reflecting geometrical, optical and structural properties. Of importance for differentiating dose/effect relationships were features of chromatin structure. In order to describe those features we developed special algorithms capable of identifying and characterizing regions of condensed chromatin as subimages. These were distinguished by their size, shape and optical density and showed typical distributions within the nucleus. As our results demonstrate, image analysis methods permit detection of DEHP related pathology in animals which, as far as is evident from routine morphologic evaluations, belong to the no-effect experimental group.

Quantitative analysis of the early changes of hepatocyte nuclei after treating Syrian golden hamsters with di(2-ethylhexyl)phthalate

Although the biological action of phthalates has been widely discussed there is little information on early cellular changes indicative for toxic or carcinogenic effects. To study subtle alterations in the cell morphology, we have by means of image processing evaluated the nuclei of hamster hepatocytes after treatment with di(2-ethylhexyl)phthalate given in single i.p. doses of 30, 300, and 3000 mg/kg. The results indicate that by using specially developed methods for analysis of images of cell nuclei and chromatin structure, it is possible to recognize changes eluding detection with usual light microscopy.