BoxCell: Leveraging SAM for Cell Segmentation with Box Supervision

November 4, 2025 · View on GitHub

Official implementation of BoxCell: Leveraging SAM for Cell Segmentation with Box Supervision published in Nature Scientific Reports paper.

📖 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.

🔬 Key Features

  • SAM Integration: Utilizes the powerful Segment Anything Model for generating high-quality segmentation proposals
  • Box Supervision: Leverages bounding box annotations for guided segmentation
  • ILP Optimization: Employs Integer Linear Programming to select optimal mask combinations
  • Multiple Solver Support: Compatible with both commercial (Gurobi) and open-source (CBC, alpha-expansion, OR-tools) solvers
  • Comprehensive Evaluation: Tested on multiple biomedical datasets (MoNuSeg, CoNSeP, TNBC)

📂 Repository Structure

BoxCell/
├── README.md
├── data-preprocessing.py     # Dataset preprocessing and format conversion
├── training-yolo.py         # YOLO model training for box detection
├── infering-yolo.py         # YOLO inference for generating bounding boxes
├── sam-ilp_opensource.py    # Main BoxCell algorithm with open-source solvers
├── sam-ilp_original.py      # Original implementation with Gurobi
├── eval-masks.py           # Evaluation metrics calculation
├── run.sh                  # Example workflow script
├── run_solver.sh          # Solver comparison script
└── segment_anything/      # SAM model implementation
    ├── modeling/          # SAM architecture components
    ├── utils/            # Utility functions
    └── ...

🚀 Quick Start

Prerequisites

  • Python 3.8+
  • PyTorch 1.9+
  • CUDA-compatible GPU

Installation

  1. Clone the repository:
git clone https://github.com/Aayushktyagi/BoxCell.git
  1. Install dependencies:
pip install torch torchvision torchaudio
pip install ultralytics  # for YOLO
pip install segment-anything-py
pip install scikit-image opencv-python matplotlib
pip install scipy numpy tqdm
pip install monai

Additionally, install dependencies from SAM

  1. Install optimization solvers:

For open-source solvers:

pip install python-mip  # includes CBC

For Gurobi (requires license):

pip install gurobipy
# Set up Gurobi license as per their documentation

Data and Pretrained Models

Download the datasets, pretrained models, and predictions (ITS and ITD) from our Google Drive.

📊 Datasets

BoxCell is evaluated on three biomedical datasets:

  • MoNuSeg: Multi-organ nuclei segmentation dataset
  • CoNSeP: Colorectal nuclear segmentation and phenotype dataset
  • TNBC: Triple-negative breast cancer dataset

🔧 Usage

1. Data Preprocessing (Optional: You can use preprocessed dataset: Google Drive)

Convert your dataset to the required format:

python data-preprocessing.py \
    --loading_dir /path/to/original/dataset \
    --saving_dir /path/to/processed/dataset \
    --dataset consep \
    --replicate True

2. Train YOLO for Box Detection

python training-yolo.py \
    --yaml_file /path/to/dataset/train.yaml \
    --model_type yolov8x \
    --num_epochs 300 \
    --batch_size 32 \
    --imgsz 500

or weights are available Google Drive

3. Generate Bounding Box Predictions

python infering-yolo.py \
    --model_weight_path /path/to/trained/yolo/weights.pt \
    --image_dir /path/to/test/images

4. Run BoxCell Segmentation

You can download SAM_Weights

With Gurobi (requires license):

python sam-ilp_original.py \
    --img_dir_path /path/to/images \
    --box_dir_path /path/to/bounding/boxes \
    --model_weights /path/to/sam/weights.pth \
    --save_path /path/to/output \
    --mode sam-ilp \
    --gurobi_license_file /path/to/gurobi.lic

With open-source solvers (recommened OR-solver):

python sam-ilp_opensource.py \
    --img_dir_path /path/to/images \
    --box_dir_path /path/to/bounding/boxes \
    --sam_s_path /path/to/sam/weights.pth \
    --save_path /path/to/output \
    --solver ortools \
    --mu 2 \
    --alpha 6 \
    --beta 25 \

solver can be: 'ortools', 'alpha_expansion', 'cbc', 'sparse'

5. Evaluate Results

python eval-masks.py \
    --gt_masks_dir /path/to/ground/truth \
    --pred_masks_dir /path/to/predictions \
    --type all

⚙️ Key Parameters

  • --mu: Weight for mask quality term (default: 2)
  • --alpha: Weight for overlap penalty (default: 6)
  • --beta: Weight for coverage reward (default: 25)
  • --lambda_val: Weight for selection regularization (default: 5)
  • --solver: Optimization solver choice (cbc, glpk, scip, gurobi)

📄 Citation

If you use BoxCell in your research, please cite our paper:

@article{tyagi2023guided,
  title={Guided Prompting in SAM for Weakly Supervised Cell Segmentation in Histopathological Images},
  author={Tyagi, Aayush Kumar and Mishra, Vaibhav and others},
  journal={arXiv preprint arXiv:2311.17960},
  year={2023}
}

Acknowledgments