3DLAND: 3D Lesion Abdominal Anomaly Localization Dataset

This repository accompanies the 3DLAND project — a large-scale, organ-aware 3D lesion segmentation benchmark for abdominal CT scans — submitted for review to ACM Multimedia 2025.

🌐 Overview

• 6,000+ contrast-enhanced CT studies
• 3D lesion masks aligned with 7 abdominal organs
• Prompt-based annotation and propagation pipeline
• Applications: anomaly detection, lesion retrieval, organ-aware analysis

🧠 Pipeline

The lesion segmentation pipeline includes:

1. Organ segmentation via MONAI and lesion-to-organ assignment
2. 2D mask generation using SAM prompts
3. 3D mask propagation using MedSAM2

📦 Dataset

We curated over 6,000 contrast-enhanced abdominal CT scans from the publicly available DeepLesion dataset, selecting only those studies that include visible lesions or anomalies in abdominal organs.

To transform these raw scans into a structured, organ-aware 3D segmentation benchmark, we developed a multi-stage pipeline with both automated and expert-in-the-loop components:

1. Organ Segmentation: We used MONAI models trained on TotalSegmentator to segment seven abdominal organs — liver, kidneys, pancreas, spleen, stomach, and gallbladder. 1.2. Lesion-to-Organ Assignment: Lesions were matched to the most probable organ based on IoU overlap and 3D proximity, with ambiguous cases reviewed by clinicians.
2. 2D Lesion Mask Generation: Using MedSAM1, we generated lesion masks from DeepLesion’s bounding boxes. We found that shrinking the box to 70% of its original size, along with a center point prompt, significantly improved segmentation precision.
3. 3D Mask Propagation: The resulting 2D masks were propagated across slices using MedSAM2, producing dense 3D segmentations with anatomical continuity.

Each lesion in the dataset is:

• Annotated in 2D on the slice where the lesion is most clearly visible within the CT series
• Localized in 3D across all slices where the lesion is present and discernible
• Assigned to a specific abdominal organ
• Each 3D segmentation mask is saved as a stack of 2D PNG slices, preserving spatial consistency across the volume

The dataset includes:

• Phase II/2D_lesion_mask:2D lesion masks linked to organs
• Pahse III/3D_lesion_mask: 3D lesion masks linked to organs
• deeplesion_Info.csv: CSV file of Our dataset metadata according to DeepLesion metadata

All annotations underwent clinical review on 10–20% of lesions per organ to ensure high-quality ground truth.

📑 Metadata CSV Format

Each lesion in the 3DLAND dataset is described in a structured CSV file that includes key metadata for localization and segmentation. This CSV file links the image slices with their corresponding organ labels and bounding boxes.

📄 Sample Columns

Column	Description
series	Series ID from the DeepLesion dataset
slice_range	Range of axial slices in which the lesion may appear (according to deeplesion dataset metadata)
key_slice	Central slice with the most visible view of the lesion
lesion_id	Unique ID assigned to each lesion
matched_organs	Organ to which the lesion is anatomically linked
File_name	PNG file name of the key slice (e.g., 000002_02_01_050.png)
Bounding_boxes	Coordinates of the lesion in the key slice: [x_min, y_min, x_max, y_max]

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📁 Folder Structure for Masks

📌 Phase II

• Location: Phase II/2D_lesion_mask
• Content: 2D lesion masks for the key slice
• File Naming: {series}_{key_slice}.png

📌 Phase III

• Location: Phase III/3D_lesion_mask
• Content: 3D volumetric lesion masks covering the entire slice range
• File Naming: {series}_K{key_slice}/{slice number}.png

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⚠️ Notes on 3D Masks

• The 3D masks in Phase III cover the full slice range, but:
  • Only a few slices near the key slice contain non-zero segmentation.
  • Slices far from the key slice are fully black (all-zero).
• 💡 This design saves space while retaining anatomically relevant data since abdominal lesions are usually thin in the axial plane.

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📌 Usage Tips

You can use the metadata CSV to:

• 🔍 Locate and crop lesions from the key slice for training or inference
• 🧠 Generate bounding box or center point prompts for segmentation models
• 🧬 Match each lesion to its organ for multi-organ anomaly analysis
• 🖼️ Load and visualize corresponding 2D or 3D masks

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📂 Metadata File Location

• 3DLAND_Info.csv

📄 License

The dataset and outputs are licensed under CC BY 4.0.
See the full license in the LICENSE file or at creativecommons.org/licenses/by/4.0