Methods for rapid and high quality acquisition of whole slide images

Abstract

In the past two decades, whole slide imaging (WSI) has been increasingly used in clinical pathology, research and education thanks to advances in technology. However, existing digital slide scanners for WSI are incapable of efficiently scanning cytology specimens in “glass-faithful quality”. In particular, cervical cytology specimens used for cervical cancer screening need to be imaged at multiple focal planes and at high spatial resolution. So, the aim of this thesis is to develop novel methods for improving the scan efficiency of cytology specimens. Preliminary investigations narrowed the research into two directions: to optimise the scan parameters (e.g. the scan map, the focus profile map and the number of focal planes to be scanned) for scanning cytology specimens, and to investigate the fast slanted (specimen) scan. Creating an accurate scan map followed by estimating the focus profile map of the specimen can significantly reduce the scan time, but previous methods are not robust to slide artefacts such as ink marker and dusts. The first research aspect of this thesis has focused on the development of a robust method that not only creates an accurate scan map but also provides a ranked list of focus candidates required for estimating the focus map. Specifically, tiles representing field-of-views to be scanned at high resolution are located on the low resolution images and evaluated with regards to whether they contain foreground objects and how good they are as focus candidates. Four metrics were proposed for the tile evaluation: threshold index (TI) that measures the image intensity; normalised auto-correlation index (NACI) that measures the spatial image similarity; auto-phase correlation index (APCI) that measures the image phase diversity; and entropy index (EI) that measures the predictability of image intensities. The experimental results indicated that while NACI, APCI and EI are effective for specimen delineation, only APCI is capable of selecting superior focus candidates and ignoring artefacts. Knowing the three-dimensional distribution of the specimen can help to determine the minimal number of focal planes to be acquired, and hence the minimal scan time. A method has been developed to evaluate the thickness of all cell and cell clumps in cervical cytology specimens incorporating an exhaustive high-resolution scan, an over-complete wavelet transform across multi-focal planes and a cell clump segmentation method. The accuracy and usefulness of the method was evaluated and demonstrated by quantitative analysis of ten Pap stained Thin-prep cervical slides. In particular, it was found that creating a focus profile map was able to reduce the number of scanning focal planes from 25.4 to 21.4 on average. It was also shown that the distribution of cells was skewed towards the cover-slip (top of the slide), so by considering the thickness of the specimen, an improved focal map can be produced to further reduce the required number of 1 micron spaced focal planes to 18.6. The last research aspect of this thesis investigated the slanted scan method, which is a promising method specifically designed for rapid scan of thick (cytology) specimens. With the method, the slide is slanted at a small angle so that cross sections of the specimen can be imaged while the specimen is moved continuously. Preliminary study concluded that the slanted scan is capable of achieving higher throughput rates than that of the conventional methods with the constraints on camera frame rates, stage accuracy and illumination intensity. However, the method suffers from optical aberrations induced by the slide slant, a two-stage deconvolution method was therefore developed to correct these aberrations. Specifically, phase deconvolution is initially applied to diminish effects of the dominating coma aberration, followed by a conventional deconvolution method to improve lost image contrast. A calibration method has also been proposed to estimate the coma aberration and the point-spread-function (PSF) of the optics utilising actual cytology specimens. The efficacy of proposed algorithms was quantitatively assessed on simulated data and qualitatively on cervical cytology specimens. Results demonstrated both an improved convergence speed of the two-stage approach, especially when correcting the bend in the PSF, and a resultant image quality that was comparable to a conventionally (flat) scanned specimen. In summary, the combination of methods proposed in this thesis have the potential to increase both overall scan efficiency and scan quality of whole slide scanners when acquiring “glass-faithful quality” images of cervical cytology specimens.