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

Effects of harvest maturity and Precooling on fruit quality and longevity of 'Bursa Si·yahi' figs (Ficus carica L.)

'Bursa Siyahi' is a purplish black and round shaped large fresh fig variety. It has a short neck, a short stalk and a, small ostiole that is well closed by the scales. The thin and firm rubbery texture of the skin of 'Bursa Siyahi' fig is important for transport. The skin has a waxy appearance and almost no cracks or checking. The meat is thin, firm and white. The pulp has no hollow at the center. The colour of mature pulp is dark red. The ripe fruit has a highly flavored taste. Unripe 'Bursa Siyahi' fig fruits with twice the firmness compared to the ripe ones showed a reduction in quality. Harvesting of figs about two days before ripening caused 20% loss in fruit weight and 9% loss in specific gravity. The taste of these fruits that had less soluble solids and sugars but higher titratable acidity was poor. In addition, the skin and pulp colors of unripe figs did not develop completely. The anthocyanin intensity was lower in these figs compared to ripe ones. Variations between the ripe and unripe figs continued in parallel after harvest and during storage as well. The respiration rates of unripe fruits at 20°C were higher than that of ripe ones. There was no significant change in respiration drift in time. Precooling decreased the weight loss during storage at 0°C and doubled the storage life to 4 weeks compared to unprecooled ones. The ripe fruits at 20°C were found to be marketable up to 4 days

Studies on fruit development and cellular morphology of quinces [Ayvalarda meyve gelişmesi ve hücresel yapinin degişimi]

This study was conducted to investigate the fruit development and cellular morphology of some quince cultivars selected in Ege Region of Turkey. During the developing period from fullbloom to harvest maturity, fruit diameter increased linearly but fruit weight followed in simple sigmoid curve. The dimensions of radial epidermal and tangential hypodermal cells increased at the same rate and 4-6 fold, isodiametric paranchymatic cells 7 fold. In mature fruit, they were 20-25 × 40-80 µm, 25-40 × 70-100 µm and 300 µm, respectively. The cell number on fruit flesh thicknes has increased from 40 to 110 in 6 weeks from fullbloom and then unchanged. Fruit flesh has starch granules with 2-5 lobes, more tannin cells, sclereid cell groups and bicolateral vessels

Post-harvest calcium and boron Treatments on retranslocation of Ca from senescent apple leaves

The objective of the study is to investigate the effect of foliar Ca and B application in autumn on re-translocation level of Ca from senescent apple leaves. In this context, it was hypothesized that foliar B application together with Ca would enhance the translocation of Ca via synergistic relation between Ca and B. To study the hypothesis, an experiment was conducted for two years in two 'Starking Delicious' apple (Malus domastica Borkh.) orchards established on seedling rootstocks in Banaz-Usak/Turkey. Treatments were composed of postharvest foliar sprays of Ca (CaCl2, 1 %), B (H3BO3, 0.5 %), and their combination (Ca+B) compared with control trees sprayed with water. Falling leaves (in November) and summer leaves (in July) were sampled and analyzed for their Ca, B, K and Mg contents. Post-harvest Ca+B treatments resulted in lower Ca concentration in the fallen leaves compared to single Ca treatments. Treatments decreased K content and did not affect Mg content of fallen leaves. Results revealed that Ca and B application increased re-translocation of Ca and B. © by PSP Volume 23 - No 9a. 20l4