Zoomify histology
![zoomify histology zoomify histology](https://image.slidesharecdn.com/epitheliumppt-160106144533/95/epithelium-ppt-6-638.jpg)
Our prototype system proved to be a successful proof-of-concept, demonstrating that even conventional approaches to image segmentation and classification had the potential not only to distinguish normal (or “wild-type”) tissue from abnormal, but also to classify the abnormality according to different levels of severity, yielding a “semi-quantitative” result. 4 for examples of normal versus mutant eye histology). In 2007, we developed the first system for automated segmentation, feature extraction, and classification of zebrafish histological abnormalities, with a pilot study focusing specifically on the larval-stage eye and gut organs, which were chosen because of their inherent polarity and “directional” organization that, when disrupted, results in mutant phenotypes that are relatively easy for human experts to detect (see Fig. We have been actively researching methods in content-based image retrieval (CBIR) and annotation with the goal of developing a fully automated system that is not only capable of scoring defects in zebrafish histology, but is also compatible with the high-throughput histology workflow that we have previously proposed (see Fig. Therefore, in order to maximize the effectiveness of histological studies as applied to animal model systems, it is critical that some form of automatic, quantitative method be developed for the analysis of histology images. While useful clinically, the qualitative aspects of current histological assessments can be associated with intra- and inter-observer variability due to variations in observer training, ability, timing, experience, and alertness. While recent technological advancements have enabled the largely automatic collection of high-throughput histological data in the form of libraries of high-resolution “virtual slides” of zebrafish larval histology , the annotation and scoring of histological data has remained a manual, subjective, and relatively low-throughput process. 1 and 2, respectively, for examples of gross versus histological images of both normal and abnormal zebrafish larvae).Ĭompared to gross phenotypic characterization using stereomicroscopy, the microscopic analysis of histological samples is more expensive in terms of time and effort. Recognizing that conventional visual morphological defect detection by gross observation using stereo-microscopy has limited sensitivity for phenotype detection at the cellular level, Zebrafish Phenome Project researchers have reached a consensus (through community meetings) that high-resolution histological approaches should be used to characterize subtle cellular and tissue-level defects that are only apparent at sub-micron resolution (see Figs. One of the key phenotyping areas proposed by researchers participating in the Zebrafish Phenome Project is that of early development-that is, from 0 to 8 days post-fertilization (dpf). The Zebrafish Phenome Project , currently in the planning stages, has a goal of functionally annotating the zebrafish genome, which presently is believed to encompass at least 20,000–25,000 genes , by systematically phenotyping mutants for each of these genes. The emerging field of phenomics, or more specifically, high-throughput phenomics , addresses the problem of collecting, integrating, and mining phenotypic data from genetic manipulation experiments across animal models. In addition, its millimeter-length scale allows whole-body phenotyping at cell resolutions, which is unique among well-characterized vertebrate model systems (Cheng lab, unpublished). Its transparent, readily accessible embryo develops ex vivo (outside the mother’s body), and most organ systems are well differentiated by seven days post-fertilization , which allows mutant phenotypes (i.e., observable traits) to be readily identified in a relatively short amount of time compared with other vertebrate model systems, such as the rat and mouse. The zebrafish has proven to be an excellent model organism for studying vertebrate development and human disease for a number of reasons. The function of uncharacterized human genes can be elucidated by studying phenotypes associated with deficiencies in homologous genes in model organisms such as the mouse, fruit fly, and zebrafish.