Machine Learning Methods and Software for Quality Control of Digital Pathology Microanatomic Segmentation


Segmentation of nuclei in whole slide images is a common methodology in pathology image analysis. A variety of anatomical segmentation methods have been developed to detect the location of nuclei and other cellular structures.  Achieving accurate and robust segmentation results remains a difficult problem because of image noise. Therefore it is necessary to have a quality control stage to assess the quality of segmentation results before the results are used in further analysis for discovery or interpretation.  In view of the vast amount of date contained within whole slide pathology images, universal automated error checking methods are needed to help pathologist detect bad segmentation quickly and reliably.


Researchers at Stony Brook University have developed a system for performing quality assessment of the segmentation of digital pathology images using a machine learning approach. This system is based on dividing the image into patch level texture features which are then the basis of the quality assessment. The machine learning classifier is trained using images that have been labeled by pathology experts and then partitioned into disjoint rectangular image patches. Once trained, the classification model can then be used to assess new images on a patch level, overlying a heat map as to which areas of the image of been segment adequately or poorly (Figure 1). Further Details : Wen S, Kurc TM, Gao Y, Zhao T, Saltz JH, Zhu W. A methodology for texture feature-based quality assessment in nucleus segmentation of histopathology image. J Pathol Inform 2017;8:38.


- Scalable Process: minimized computing power for Q/A assessment of large data sets - Universal application across different segmentation algorithms - (Semi-)Automated


- Digital pathology - Industrial applications include satellite and astronomical image data analysis.

Patent Status

Patent application submitted

Stage Of Development

PCT covering methods and system for determining segmentation quality

Licensing Potential


Licensing Status


Additional Info ZEN browser for Virtual Microscopy, ZEISS Microscopy, CC BY-SA 2.0.
Patent Information:
Case ID: R050-8922
For Information, Contact:
Sean Boykevisch
State University of New York at Stony Brook
Joel Haskin Saltz
Tahsin Kurc
Yi Gao
Wei Zhu
Si Wen
Tianhao Zhao
Sampurna Shrestha