DOI: 10.5281/zenodo.18292965
title: DeepLesion-1kTest3D

description: DeepLesion-1kTest3D Dataset Processing - Documentation


This document provides documentation for DeepLesion-1kTest3D - a 3D NIfTI conversion of 1,000 test cases from the DeepLesion dataset, enabling volumetric analysis of diverse lesion types across multiple anatomical regions.





📂 Dataset Information


Dataset Name: DeepLesion-1kTest3DSource: DeepLesion (NIH Clinical Center)Original Dataset Paper: Yan et al. (2018), "DeepLesion: automated mining of large-scale lesion annotations and universal lesion detection with deep learning"Original Format: 16-bit PNG slices (2D multi-slice representation)Converted Format: 3D NIfTI volumesTotal Test Cases: 1,000 3D CT volumesTotal Lesion Annotations: 4,927 lesions in test setProcessed By: Fakrul Islam TusharGitHub Repository: https://github.com/fitushar/HAIDZenodo NIfTI Repository: https://doi.org/10.5281/zenodo.18292965



Dataset Characteristics




Original DeepLesion: 32,735 lesions from 32,120 CT scans (10,594 patients)

Test Subset: 1,000 CT volumes with 4,927 lesion annotations

Lesion Types: 8 coarse categories (lung, liver, kidney, lymph node, bone, soft tissue, abdomen, pelvis)

Annotation Source: PACS system bookmarks from clinical radiology practice

Measurement: RECIST diameters (long/short axis measurements)

Slice Context: Variable slice range (typically 30-60 consecutive slices)




Test Set Organ-Specific Subsets




Liver Lesions: 701 liver lesion annotations (test set)

Kidney Lesions: 235 kidney lesion annotations (test set)

Other Organs: Lung, lymph nodes, bone, soft tissue, mediastinum




Coarse Lesion Type Distribution (Test Set)




Type 1: Lung nodules

Type 2: Abdomen lesions

Type 3: Mediastinum lesions

Type 4: Liver lesions

Type 5: Soft tissue lesions

Type 6: Kidney and urinary lesions

Type 7: Bone lesions

Type 8: Pelvic lesions






🔄 Processing Pipeline




1️⃣ PNG Slice Loading and 3D Volume Reconstruction


Purpose: Convert 2D 16-bit PNG slices to 3D NIfTI volumes with proper spacing

Input:



DeepLesion 16-bit PNG slices stored in patient folders

Format: Images_png/{Patient_Study_Series}/{SliceIndex}.png

Metadata: DL_info.csv with spacing and slice range information


Process:



import cv2
import numpy as np
import nibabel as nib

# Load consecutive slices
for slice_idx in slice_range:
    im = cv2.imread(f'{slice_idx:03d}.png', -1)  # -1 for 16-bit
    # Remove intensity bias from 16-bit PNG encoding
    im = (im.astype(np.int32) - 32768).astype(np.int16)
    slices.append(im)

# Stack slices into 3D volume
volume = cv2.merge(slices)  # or np.stack for >300 slices

# Create NIfTI with proper transformation matrix
spacing = [spacing_x, spacing_y, spacing_z]  # mm per pixel
T = np.array([[0, -spacing[1], 0, 0],
              [-spacing[0], 0, 0, 0],
              [0, 0, -spacing[2], 0],
              [0, 0, 0, 1]])
nifti_img = nib.Nifti1Image(volume, affine=T)
nib.save(nifti_img, output_path)

 


16-bit PNG Encoding:



DeepLesion stores CT in 16-bit PNG with intensity bias of +32768

Conversion subtracts 32768 to restore original Hounsfield Units (HU)

Resulting range: -1024 to +3071 HU (typical CT window)


Output:



3D NIfTI files: DeepLesion-1KTest-3D/{Patient_Study_Series}_SliceStart-SliceEnd.nii.gz

Format example: 000001_01_01_103-115.nii.gz (Patient 1, Study 1, Series 1, slices 103-115)

Total: 1,000 NIfTI volumes






2️⃣ Metadata and Lesion Annotation Integration


Purpose: Link 3D volumes with lesion annotations, measurements, and clinical metadata

Input:



Original DeepLesion metadata: DL_info.csv

Test split assignment

RECIST measurements (long/short axis)


Process:



Parse DeepLesion metadata CSV

Extract key slice index (slice with measurement annotation)

Map PNG file names to 3D NIfTI volumes

Preserve RECIST diameter measurements

Extract normalized lesion locations (0-1 coordinates)

Assign coarse lesion type labels (1-8)


Metadata Fields:



File_name: Original 2D PNG key slice (e.g., 000001_01_01_109.png)

Patient_index: Unique patient identifier (1-10594)

Study_index: Study number for patient (multiple studies per patient)

Series_ID: Series within study

Key_slice_index: Central slice with measurement annotation

Measurement_coordinates: RECIST long/short axis endpoints (x1,y1,x2,y2,x3,y3,x4,y4)

Bounding_boxes: Lesion bounding box (xmin,ymin,xmax,ymax)

Lesion_diameters_Pixel: Long and short axis lengths in pixels

Normalized_lesion_location: 3D normalized coordinates (0-1 range)

Coarse_lesion_type: Lesion category (1=lung, 2=abdomen, 3=mediastinum, 4=liver, 5=soft tissue, 6=kidney, 7=bone, 8=pelvis)

Possibly_noisy: Quality flag (0=clean, 1=potentially noisy annotation)

Slice_range: First and last slice indices in volume

Spacing_mm_px: Pixel spacing (x, y, z) in mm

Image_size: Image dimensions (typically 512×512)

DICOM_windows: Display window (level, width)

Patient_gender: M/F

Patient_age: Age at scan

Nifti_ct_name: Corresponding 3D NIfTI filename


Output Files:



DL_info_niftiID_test.csv (4,928 lesion annotations in test set)

test_Cases_list_DLplus_df.csv (801 unique test cases)

DeepLesion_Liver_test_set.csv (702 liver lesions)

DeepLesion_Kidneys_test_set.csv (236 kidney lesions)






3️⃣ Transformation Matrix for 3D Visualization


Purpose: Create proper affine transformation for correct display in 3D Slicer and ITK-SNAP

Transformation Matrix:



T = [[0,        -spacing_y,  0,           0],
     [-spacing_x, 0,          0,           0],
     [0,         0,          -spacing_z,  0],
     [0,         0,          0,           1]]


 


Rationale:



DeepLesion uses axial slice ordering (superior to inferior)

Negative spacing ensures proper anatomical orientation

Compatible with 3D Slicer and ITK-SNAP viewers

Preserves patient coordinate system


Visualization:



3D Slicer: Load NIfTI volumes directly with correct orientation

ITK-SNAP: Lesion annotations can be overlaid using bounding boxes

Manual inspection: Verify lesion location matches key slice index






4️⃣ Organ-Specific Subset Extraction


Purpose: Create focused subsets for liver and kidney lesion research

Liver Lesion Subset:



Count: 701 liver lesion annotations (test set)

Coarse type: Label 4 (liver)

Use cases: Liver tumor detection, liver metastasis analysis

File: DeepLesion_Liver_test_set.csv


Kidney Lesion Subset:



Count: 235 kidney lesion annotations (test set)

Coarse type: Label 6 (kidney/urinary)

Use cases: Renal mass characterization, kidney cyst detection

File: DeepLesion_Kidneys_test_set.csv


Extraction Criteria:



# Liver lesions
liver_lesions = df[df['Coarse_lesion_type'] == 4]

# Kidney lesions
kidney_lesions = df[df['Coarse_lesion_type'] == 6]

 






📊 Dataset Statistics




Test Set Overview




Total NIfTI Volumes: 1,000 3D CT scans

Total Lesion Annotations: 4,927 lesions

Lesions per Volume: 1-10+ lesions (variable)

Unique Patients: ~400-500 patients (accounting for follow-up scans)




Slice and Spacing Characteristics




Slice Range: Typically 30-60 consecutive slices per volume

Shortest volume: ~12 slices

Longest volume: ~270 slices (extended abdomen/pelvis)

In-plane Spacing: 0.31 - 0.98 mm/pixel (variable resolution)

Slice Thickness: 1.0 - 5.0 mm (most common: 5mm)

Image Size: 512×512 pixels (consistent)




Lesion Size Distribution




Small lesions: <10mm diameter (~30%)

Medium lesions: 10-30mm diameter (~50%)

Large lesions: >30mm diameter (~20%)

RECIST measurements: Both long axis and short axis provided




Clinical Demographics




Age Range: 11-87 years (diverse adult and pediatric population)

Gender: Mixed male/female cohort

Clinical Context: Real-world radiology practice bookmarks




Anatomical Distribution (Test Set)




Liver (Type 4):         701 lesions (~14%)
Kidney (Type 6):        235 lesions (~5%)
Lung (Type 1):          ~1,500 lesions (~30%)
Lymph Nodes (Type 3):   ~800 lesions (~16%)
Bone (Type 7):          ~600 lesions (~12%)
Soft Tissue (Type 5):   ~500 lesions (~10%)
Abdomen (Type 2):       ~400 lesions (~8%)
Pelvis (Type 8):        ~191 lesions (~4%)


 




Image Quality Flags




Clean annotations: ~95% (Possibly_noisy=0)

Potentially noisy: ~5% (Possibly_noisy=1)

Noisy annotations: Ambiguous lesion boundaries or measurement inconsistencies






🗂️ File Structure




DeepLesion/
├── 036501_1.pdf                                  # Original DeepLesion paper
├── DL_save_nifti.py                              # PNG-to-NIfTI conversion script
│
├── DL_info.csv                                   # Full DeepLesion metadata (32,735 lesions)
├── DL_info_niftiID.csv                           # Metadata with NIfTI filenames
├── DL_info_niftiID_test.csv                      # Test set metadata (4,928 lesions)
│
├── test_Cases_list_DLplus_df.csv                 # Test set NIfTI volume list (801 cases)
├── val_Cases_list_DLplus_df.csv                  # Validation set NIfTI volume list
│
├── DeepLesion_Liver_test_set.csv                 # Liver lesion subset (702 lesions)
├── DeepLesion_Kidneys_test_set.csv               # Kidney lesion subset (236 lesions)
│
├── DeepLesion-1KTest-3D/                         # 3D NIfTI test volumes
│   ├── 000001_01_01_103-115.nii.gz               # Patient 1, Study 1, Series 1
│   ├── 000001_03_01_058-118.nii.gz
│   ├── 000016_01_01_019-036.nii.gz
│   └── ... (1,000 NIfTI files)
│
└── DeepLesion-1KTest-3D.zip                      # Zenodo upload archive
    └── Zenodo Repository: https://doi.org/10.5281/zenodo.18292965


 






🛠️ Software Dependencies




Core Libraries




opencv-python (cv2) 4.5.0+ (16-bit PNG reading)

nibabel 3.2.0+ (NIfTI creation and saving)

numpy 1.20.0+ (Array operations)

pandas 1.3.0+ (Metadata management)




Optional Visualization




3D Slicer 4.11+ (3D volume visualization)

ITK-SNAP 3.8+ (Lesion annotation overlay)




Installation




# Core dependencies
pip install opencv-python>=4.5.0 nibabel>=3.2.0 numpy>=1.20.0 pandas>=1.3.0

# Optional visualization tools
# Download 3D Slicer: https://download.slicer.org/
# Download ITK-SNAP: http://www.itksnap.org/

 






📈 Processing Highlights




PNG-to-NIfTI Conversion Advantages




3D Visualization: Enable volumetric viewing in 3D Slicer and ITK-SNAP

Spatial Context: Preserve anatomical relationships across slices

Standardized Format: NIfTI is widely supported by medical imaging tools

Metadata Preservation: Affine transformation encodes spacing and orientation




16-bit PNG Intensity Correction




Original: PNG stores values 0-65535

Bias: +32768 offset for signed 16-bit representation

Corrected: Subtract 32768 → -32768 to +32767 (Hounsfield Units)

Clinical relevance: Restored HU enables window/level visualization




Lesion Annotation Format




RECIST Measurements: Standard oncology response criteria

Bounding Boxes: Tight rectangular regions around lesions

Normalized Locations: 3D coordinates normalized to 0-1 range (body coverage)

Key Slice: Central slice with measurement annotation




Multi-Lesion Volumes




Many volumes contain multiple lesions (2-10+ lesions per scan)

Each lesion has independent annotation entry

Same NIfTI volume referenced multiple times in metadata

Enables comprehensive lesion detection benchmarking






🔗 Related Resources




Original DeepLesion Paper: Yan et al. (2018), IEEE J. Biomed. Health Inform.

DeepLesion Dataset: https://nihcc.app.box.com/v/DeepLesion

Zenodo NIfTI Repository: https://doi.org/10.5281/zenodo.18292965

Processing Code: https://github.com/fitushar/HAID

Processed By: Fakrul Islam Tushar






📝 Citation


If you use this pre-processed dataset, please cite:





Original DeepLesion Paper:



Yan, K., Wang, X., Lu, L., & Summers, R. M. (2018). 
DeepLesion: automated mining of large-scale lesion annotations and universal lesion detection with deep learning. 
Journal of Biomedical and Health Informatics, 22(4), 1091-1101.
DOI: 10.1109/JBHI.2017.2780066


 





DeepLesion Dataset:



Yan, K., et al. (2018). 
DeepLesion: Large-scale Lesion Annotations from CT with Deep Learning.
NIH Clinical Center: https://nihcc.app.box.com/v/DeepLesion


 





DeepLesion-1kTest3D (3D NIfTI Conversion):



Fakrul Islam Tushar. (2026). 
DeepLesion-1kTest3D: 3D NIfTI Conversion of DeepLesion Test Set.
Zenodo: https://doi.org/10.5281/zenodo.18292965
GitHub: https://github.com/fitushar/HAID


 








📌 Notes


3D Conversion: Complete PNG-to-NIfTI conversion for 1,000 test casesLesion Annotations: 4,927 diverse lesion annotations with RECIST measurementsOrgan-Specific Subsets: Liver (701) and kidney (235) lesion subsets availableTransformation Matrix: Optimized for 3D Slicer and ITK-SNAP visualization16-bit Intensity Correction: Proper Hounsfield Unit restoration (-32768 bias removal)Multi-Lesion Volumes: Many volumes contain multiple annotated lesionsZenodo Repository: All 1,000 3D NIfTI volumes publicly available at https://doi.org/10.5281/zenodo.18292965



Document Version: 1.0Last Updated: January 18, 2026Processed By: Fakrul Islam TusharContact: GitHub - https://github.com/fitushar/HAID