Classifying breast cancer and fibroadenoma tissue biopsies from paraffined stain-free slides by fractal biomarkers in Fourier Ptychographic Microscopy

Abstract

Breast cancer is one of the most spread and monitored pathologies in high-income countries. After breast biopsy, histological tissue is stored in paraffin, sectioned and mounted. Conventional inspection of tissue slides under benchtop light microscopes involves paraffin removal and staining, typically with H&E. Then, expert pathologists are called to judge the stained slides. However, paraffin removal and staining are operator-dependent, time and resources consuming processes that can generate ambiguities due to non-uniform staining. Here we propose a novel method that can work directly on paraffined stain-free slides. The method is automatic, independent from the operator, and provides classification of different portions of the tissue image with very high accuracy. Besides, it returns a guide map to help pathologist to judge the different tissue portions based on the likelihood these can be associated to a breast cancer or fibroadenoma biomarker. We use Fourier Ptychography as a quantitative phase-contrast microscopy method, which allows accessing a very wide field of view (i.e., square millimeters) in one single image while guaranteeing at the same time high lateral resolution (i.e., 0.5 microns). This imaging method is multi-scale, since it enables looking at the big picture, i.e. the complex tissue structure and connections, with the possibility to zoom-in up to the single cell level. In order to handle this informative image content, we introduce elements of fractal geometry as a multi-scale analysis method. We show the effectiveness of fractal features in describing fibroadenoma and breast cancer from six patients with very high accuracy. The proposed method could significantly simplify the steps of tissue analysis and make it independent from the sample preparation, the skills of the lab operator and the pathologist.

Methods for imaging and analysis of hystological tissue slides via Fourier Ptychographic Microscopy

“…The staining process used for further analyses follows the proper protocols [5]. The frog neural tissue is a sample stained with H&E. The fibroadenoma and breast cancer tissue slides were processed by the routine Logos Milestone microwave processor without removing paraffine [16]. In Fig.…”

“…In case of fibroadenoma and breast cancer, paraffined tissue slides underwent the FPM process and the wrapped FPM phase maps have been analyzed by using fractal geometry [18,16]. The fractal feature extraction is based on binary images calculated from the pattern of phase jumps of the FPM phasecontrast maps of the tissues.…”

“…In this regard, we show a method to analyze paraffined tissue slides, in particular applied here to stainfree breast tissue. The method is based on elements of fractal geometry for classification purposes [16]. Wraps patterns are conveniently used for such fractal analysis.…”