Lymphocyte Annotator: CD3+ and CD8+ IHC Stained Patch Image Annotation Tool

In digital pathology, preliminary step for the development of Computer Aided Diagnostics involves defining and labelling an Object of Interest. Contrary to traditional tiresome method of observation and marking of objects under microscope, digital pathology enables the use of annotation tools to capture localization information and morphology for targeted object(s). However, it is quite difficult to capture this information due to high inter and intra class variance. In this paper, we have addressed these two different problems by developing an easy to use and efficient tool "Lymphocyte Annotator" that allows a user to draw bounding box(es) on IHC stained images, and as a result, automatically generates multiple variants of segmentation masks for the targeted object. Lymphocyte Annotator provides multiple options for bounding box selection, with variation in bounding box size and type. The developed tool targets labelling of lymphocytes in histopathological images. This annotator generates five different types of masks by using a) Chan Vese Segmentation Model, b) Morphological Active Contours without Edges Model, c) Morphological Geodesic Active Contours Model, d) Adaptive Thresholding and e) Circular Masks, thus providing user with an opportunity to use a mixture of different types of generated masks. Capturing of lymphocytes' morphology using different models incorporates morphological variance and enables training of robust deep Convolutional Neural Network. The annotations created from this tool are by default exported in PASCAL VOC and JSON format. Lymphocyte annotator is an open-source tool, and can be accessed from source, available at https://github.com/m-mohsin-zafar/lysto_labeltool.