BoxCell: Leveraging SAM for Cell Segmentation with Box Supervision

Aayush Kumar Tyagi, Vaibhav Mishra, Prathosh A.P., Mausam

Abstract: Cell segmentation in histopathological images is vital for diagnosis, and treatment of several diseases. Annotating data is tedious, and requires medical expertise, making it difficult to employ supervised learning. Instead, we study a weakly supervised setting, where only bounding box supervision is available, and present the use of Segment Anything (SAM) for this without any finetuning, i.e., directly utilizing the pre-trained model. We propose BoxCell, a cell segmentation framework that utilizes SAM’s capability to interpret bounding boxes as prompts, both at train and test times. At train time, gold bounding boxes given to SAM produce (pseudo-)masks, which are used to train a standalone segmenter. At test time, BoxCell generates two segmentation masks: (1) generated by this standalone segmenter, and (2) a trained object detector outputs bounding boxes, which are given as prompts to SAM to produce another mask. Recognizing complementary strengths, we reconcile the two segmentation masks using a novel integer programming formulation with intensity and spatial constraints. We experiment on three publicly available cell segmentation datasets namely, CoNSep, MoNuSeg, and TNBC, and find that BoxCell significantly outperforms existing box supervised image segmentation models, obtaining 6-10 point Dice gains.

External IDs:doi:10.1038/s41598-025-26789-1