PythoStitcher: an iterative approach for stitching digitized tissue fragments into full resolution whole-mount reconstructions

In histopathology, whole-mount sections (WMS) can be utilized to capture entire cross-sections of excised tissue, thereby reducing the number of slides per case, preserving tissue context, and minimizing cutting artefacts. Additionally, the use of WMS allows for easier correlation of histology and pre-operative imaging. However, in digital pathology, WMS are not frequently acquired due to the limited availability of whole-slide scanners that can scan double-width glass slides. Moreover, whole-mounts may still be too large to fit on a single double-width glass slide, and archival material is typically stored as tissue fragments. In this work, we present PythoStitcher, an improved version of the AutoStitcher algorithm for automatically stitching multiple tissue fragments and constructing a full-resolution WMS. PythoStitcher is based on a genetic algorithm that iteratively optimizes the affine transformation matrix for each tissue ...