This pipeline is designed for image patch and whole slide level nuclei detection, segmentation and TME feature extraction. The pipeline uses HD-Yolo algorithm by default for real-time nuclei segmentation cross the whole slide and utilize the results for TME feature analysis. There are three main functions/components in this repo. A docker image here contains all the code, model, and test data.
We introduce ScopeViewer, a browser-based software designed to visualize large image data and associated annotations at various zoom levels, allowing for intricate exploration of the data; enable dual interactive viewing of the original images along with their annotations, providing a comprehensive understanding of the context; display spatial molecular features with optimized band-width, ensuring a smooth user experience; and bolster data security by circumventing data transfers.