Automated detection of regions of interest for tissue microarray experiments: an image texture analysis

BACKGROUND: Recent research with tissue microarrays led to a rapid progress toward quantifying the expressions of large sets of biomarkers in normal and diseased tissue. However, standard procedures for sampling tissue for molecular profiling have not yet been established. METHODS: This study presents a high throughput analysis of texture heterogeneity on breast tissue images for the purpose of identifying regions of interest in the tissue for molecular profiling via tissue microarray technology. Image texture of breast histology slides was described in terms of three parameters: the percentage of area occupied in an image block by chromatin (B), percentage occupied by stroma-like regions (P), and a statistical heterogeneity index H commonly used in image analysis. Texture parameters were defined and computed for each of the thousands of image blocks in our dataset using both the gray scale and color segmentation. The image blocks were then classified into three categories using the texture feature parameters in a novel statistical learning algorithm. These categories are as follows: image blocks specific to normal breast tissue, blocks specific to cancerous tissue, and those image blocks that are non-specific to normal and disease states. RESULTS: Gray scale and color segmentation techniques led to identification of same regions in histology slides as cancer-specific. Moreover the image blocks identified as cancer-specific belonged to those cell crowded regions in whole section image slides that were marked by two pathologists as regions of interest for further histological studies. CONCLUSION: These results indicate the high efficiency of our automated method for identifying pathologic regions of interest on histology slides. Automation of critical region identification will help minimize the inter-rater variability among different raters (pathologists) as hundreds of tumors that are used to develop an array have typically been evaluated (graded) by different pathologists. The region of interest information gathered from the whole section images will guide the excision of tissue for constructing tissue microarrays and for high throughput profiling of global gene expression

Estimation of viscous dissipation inside an erythrocyte during aspirational entry into a micropipette.

Viscous dissipation inside the erythrocyte during its aspirational entry into a micropipette is analyzed. The motion of the intracellular fluid is approximated by a flow into the micropipette orifice from a half space (the portion of the erythrocyte outside the micropipette). The stream function and intracellular pressure (p) in the half space are obtained as a function of radial and axial positions near the orifice. Solution of the boundary value problem for a uniform stream entering a circular hole gives p = 2 eta HQ/pi R3p, where eta H is the intracellular viscosity, Q is the total discharge, and Rp is the pipette radius. The results indicate that the moving erythrocyte membrane helps to drive the intracellular fluid into the orifice. For normal erythrocytes, p is only approximately 0.5% of the total aspiration pressure (delta P). The contribution of p to delta P, however, may become significant when there is a large increase in eta H due to a markedly elevated intracellular hemoglobin concentration or an alteration of the physical state of hemoglobin

Passive mechanical properties of human leukocytes.

Micropipette experiments are used to determine the rheological properties of human leukocytes. Individual cells in EDTA are subjected to a known aspiration pressure via a micropipette, and their surface deformation from the undeformed spherical shape is recorded on a television monitor. The cells are mathematically modeled as homogeneous spheres, and a standard solid viscoelastic model is found to describe accurately the deformation of the cell for small strains. These experimental and theoretical studies provide the basis for further investigations of leukocyte rheology in health and disease

New horizons in reconstructing past human behavior : introducing the “Tübingen University Validated Entheses-based Reconstruction of Activity” method

An accurate reconstruction of habitual activities in past populations and extinct hominin species is a paramount goal of paleoanthropological research, as it can elucidate the evolution of human behavior and the relationship between culture and biology. Variation in muscle attachment (entheseal) morphology has been considered an indicator of habitual activity, and many attempts have been made to use it for this purpose. However, its interpretation remains equivocal due to methodological shortcomings and a paucity of supportive experimental data. Through a series of studies, we have introduced a novel and precise methodology that focuses on reconstructing muscle synergies based on three-dimensional and multivariate analyses among entheses. This approach was validated using uniquely documented anthropological samples, experimental animal studies, histological observations, and geometric morphometrics. Here, we detail, synthesize, and critically discuss the findings of these studies, which overall point to the great potential of entheses in elucidating aspects of past human behavior