A c c e p t e d M a n u s c r i p tWe developed an algorithm to estimate the thickness of cervical cytology specimens.The proposed algorithm reached an accuracy of 1 micron at 90% of times.The algorithm was used to quantitatively analysis of ten normal Thin-prep cervical cytology slides.It was found that the distribution of cells is skewed towards the cover-slip (top of the slide).It was also proved that considering the thickness of focal points produced focus maps in superior qualities compared to conventional ones.
Highlights (for review)Page 2 of 28 A c c e p t e d M a n u s c r i p t
AbstractKnowledge of the spatial distribution and thickness of cytology specimens is critical to the development of digital slide acquisition techniques that minimise both scan times and image file size. In this paper, we evaluate a novel method to achieve this goal utilising an exhaustive high-resolution scan, an over-complete wavelet transform across multi-focal planes and a clump segmentation of all cellular material on the slide. The method is demonstrated with a quantitative analysis of ten normal, but difficult to scan Pap stained, Thin-prep, cervical cytology slides. We show that with this method the top and bottom of the specimen can be estimated to an accuracy of 1 micron in 88% and 97% of the fields of view respectively. Overall, cellar material can be over 30 microns thick and the distribution of cells is skewed towards the cover-slip (top of the slide). However, the median clump thickness is 10 microns and only 31% of clumps contain more than three nuclei. Therefore, by finding a focal map of the specimen the number of 1 micron spaced focal planes that are required to be scanned to acquire 95% of the in-focus material can be reduced from 25.4 to 21.4 on average. In addition, we show that by considering the thickness of the specimen, an improved focal map can be produced which further reduces the required number of 1 micron spaced focal planes to 18.6. This has the potential to reduce scan times and raw image data by over 25%.