TY  - JOUR
AU  - Ester, Oliver
AU  - Hörst, Fabian
AU  - Seibold, Constantin
AU  - Keyl, Julius
AU  - Ting, Saskia
AU  - Vasileiadis, Nikolaos
AU  - Schmitz, Jessica
AU  - Ivanyi, Philipp
AU  - Grünwald, Viktor
AU  - Bräsen, Jan Hinrich
AU  - Egger, Jan
AU  - Kleesiek, Jens
TI  - Valuing vicinity: Memory attention framework for context-based semantic segmentation in histopathology.
JO  - Computerized medical imaging and graphics
VL  - 107
SN  - 0895-6111
CY  - Amsterdam [u.a.]
PB  - Elsevier Science
M1  - DKFZ-2023-01009
SP  - 102238
PY  - 2023
AB  - The segmentation of histopathological whole slide images into tumourous and non-tumourous types of tissue is a challenging task that requires the consideration of both local and global spatial contexts to classify tumourous regions precisely. The identification of subtypes of tumour tissue complicates the issue as the sharpness of separation decreases and the pathologist's reasoning is even more guided by spatial context. However, the identification of detailed tissue types is crucial for providing personalized cancer therapies. Due to the high resolution of whole slide images, existing semantic segmentation methods, restricted to isolated image sections, are incapable of processing context information beyond. To take a step towards better context comprehension, we propose a patch neighbour attention mechanism to query the neighbouring tissue context from a patch embedding memory bank and infuse context embeddings into bottleneck hidden feature maps. Our memory attention framework (MAF) mimics a pathologist's annotation procedure - zooming out and considering surrounding tissue context. The framework can be integrated into any encoder-decoder segmentation method. We evaluate the MAF on two public breast cancer and liver cancer data sets and an internal kidney cancer data set using famous segmentation models (U-Net, DeeplabV3) and demonstrate the superiority over other context-integrating algorithms - achieving a substantial improvement of up to 17
KW  - Computational pathology (Other)
KW  - Context (Other)
KW  - Histopathology (Other)
KW  - Renal cell carcinoma (Other)
KW  - Semantic segmentation (Other)
LB  - PUB:(DE-HGF)16
C6  - pmid:37207396
DO  - DOI:10.1016/j.compmedimag.2023.102238
UR  - https://inrepo02.dkfz.de/record/276187
ER  -