System for combined three‐dimensional morphological and molecular analysis of thick tissue specimens

Abstract

We present a new system for simultaneous morphological and molecular analysis of thick tissue samples. The system is composed of a computer assisted microscope and a JAVAbased image display, analysis and visualization program that allows acquisition, annotation, meaningful storage, three-dimensional reconstruction and analysis of structures of interest in thick sectioned tissue specimens. We describe the system in detail and illustrate its use by imaging, reconstructing and analyzing two complete tissue blocks which were differently processed and stained. One block was obtained from a ductal carcinoma in situ (DCIS) lumpectomy specimen and stained alternatively with Hematoxilyn and Eosin (H&E), and with a counterstain and fluorescence in situ hybridization (FISH) to the ERB-B2 gene. The second block contained a fully sectioned mammary gland of a mouse, stained for Histology with H&E.We show how the system greatly reduces the amount of interaction required for the acquisition and analysis and is therefore suitable for studies that require morphologically driven, wide scale (e.g. whole gland) analysis of complex tissue samples or cultures.2

Loss of expression of chromosome 16q genes DPEP1 and CTCF in lobular carcinoma in situ of the breast

“…In our study, the genes investigated were located on the most frequent smallest regions of deletion (SROs) at 16q (16q22.1 and 16q24.3) and are therefore considered potential target TSGs [8]. We used CDH1 as a positive control as it has previously been recognised as a TSG in lobular carcinomas [5,9,13,25]. The results presented here further support previous studies [9,[26][27][28] in suggesting that CDH1 is a TSG in LCIS, as immunohistochemistry and RT-PCR showed almost complete absence of expression compared with normal breast lobules.…”

Consistent and Elastic Registration of Histological Sections Using Vector-Spline Regularization

“…We have developed an integrated microscopy system that automates or greatly reduces the amount of interaction required for these tasks [1,2] and provides volumetric renderings of the structures in the tissue.…”

Associative image analysis: A method for automated quantification of 3D multi-parameter images of brain tissue

“…Automated algorithms have been developed to delineate individual elements of neuroanatomy, e.g., counting of nuclei, tracing neuronal processes, branching pattern of dendrites for a single neuron, and vascular tracing Lin et al, 2005a;Tyrrell JA et al, 2007;Fernandez-Gonzalez et al, 2002;Weaver et al, 2004;Lin et al, 2007;Zhang et al, 2007;Al-Kofahi et al, 2007). These tools are able to delineate a specific class of structures from single channel images with error rates in the range of 5 -10%, and have progressed greatly in their ability to handle morphological variability.…”