Image analysis tools

Many proposed histopathology image analysis methods rely in part on similar processing steps. On this page, we aim to collect a set of histopathology image analysis tools that can help the participants design and improve their methods.

Currently there is only one tool on this page but we hope to expand it soon. If you would like to contribute your own tools please contact the challenge organizers.

Staining unmixing and normalization

One of the major difficulties in histopathology image analysis is apperance variability. For example, when performing mitosis detection, many false positives can arise when the histopathology slide is overstained. This MATLAB code performs staining unmixing (separation of the hematoxylin and eosing stains) and apperance normalization. It is based on the method described in [1]. Some examples of staining normalization can be seen in the figure below.

Download (ZIP, 5.3 MB, version date 22/11/13)

[1] A method for normalizing histology slides for quantitative analysis, M Macenko, M Niethammer, JS Marron, D Borland, JT Woosley, G Xiaojun, C Schmitt, NE Thomas, IEEE ISBI, 2009. dx.doi.org/10.1109/ISBI.2009.5193250

Example staining normalization. The top row are the original images and the bottom row are the images after performing staining normalization.