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Adapting SAM to Histopathology Images for Tumor Bud Segmentation in Colorectal Cancer.

Ziyu SuWei ChenSony AnnemUsama SajjadMostafa RezapourWendy L FrankelMetin N GurcanM Khalid Khan Niazi
Published in: Proceedings of SPIE--the International Society for Optical Engineering (2024)
Colorectal cancer (CRC) is the third most common cancer in the United States. Tumor Budding (TB) detection and quantification are crucial yet labor-intensive steps in determining the CRC stage through the analysis of histopathology images. To help with this process, we adapt the Segment Anything Model (SAM) on the CRC histopathology images to segment TBs using SAM-Adapter. In this approach, we automatically take task-specific prompts from CRC images and train the SAM model in a parameter-efficient way. We compare the predictions of our model with the predictions from a trained-from-scratch model using the annotations from a pathologist. As a result, our model achieves an intersection over union (IoU) of 0.65 and an instance-level Dice score of 0.75, which are promising in matching the pathologist's TB annotation. We believe our study offers a novel solution to identify TBs on H&E-stained histopathology images. Our study also demonstrates the value of adapting the foundation model for pathology image segmentation tasks.
Keyphrases
  • deep learning
  • convolutional neural network
  • mycobacterium tuberculosis
  • squamous cell carcinoma
  • high resolution
  • working memory
  • young adults
  • body composition
  • lymph node metastasis