Lung-Fused-CT-Pathology | Fused Radiology-Pathology Lung Dataset

DOI: 10.7937/k9/tcia.2018.smt36lpn | Data Citation Required | Image Collection

Location	Species	Subjects	Data Types	Cancer Types	Size	Supporting Data	Status	Updated
Lung	Human	6	CT, Histopathology	Lung Cancer	27.21GB	Image Analyses, Software/Source Code	Public, Complete	2018/07/30

Summary

This is the first attempt of mapping the extent of Invasive Adenocarcinoma onto in vivo lung CT. The mappings constitute ground truth of disease and may be used to further investigate the imaging signatures of Invasive Adenocarcinoma in ground glass pulmonary nodules. Patient with small ground glass nodules with >2 histology slices per nodule were included. Patients with solid large nodules (>40mm), with <3 histology slices or with histology slices showing substantial artifacts were excluded from this study (see reference below for details). Data collection and analysis was provided by Case Western Reserve University.

References

All the program scripts that were used for generating the results and data in this paper have been made available at https://github.com/mirabelarusu/RadPathFusionLung
This study is described in detail in the following publication:
- Rusu M., Rajiah P., Gilkeson R., Yang M., Donatelli C., Thawani R., Jacono F.J., Linden P., Madabushi A. (2017) Co-registration of pre-operative CT with ex vivo surgically excised ground glass nodules to define spatial extent of invasive adenocarcinoma on in vivo imaging: a proof-of-concept study. European Radiology 27:10, 4209:4217. DOI: https://doi.org/10.1007/s00330-017-4813-0

Data Access

Version 1: Updated 2018/07/30

Title	Data Type	Format	Access Points	Subjects	Studies	Series	Images	License
CT Images and Histology compartments mapped on CT	SEG, CT	DICOM	Download (5.91gb) Search Download requires NBIA Data Retriever	6	36	52	11,210	CC BY 3.0
Annotated Whole Slide Pathology Images	Histopathology	TIFF	Download (21.3gb) Search Download requires IBM-Aspera-Connect plugin	6	6		25	CC BY 3.0
Clinical data		XLSX	Download (15.37kb)					CC BY 3.0

Additional Resources for this Dataset

The NCI Cancer Research Data Commons (CRDC) provides access to additional data and a cloud-based data science infrastructure that connects data sets with analytics tools to allow users to share, integrate, analyze, and visualize cancer research data.

Imaging Data Commons (IDC) (Imaging Data)
Source code is publicly available on Github at https://github.com/mirabelarusu/RadPathFusionLung

Citations & Data Usage Policy

Data Citation Required: Users must abide by the TCIA Data Usage Policy and Restrictions. Attribution must include the following citation, including the Digital Object Identifier:

	Data Citation
	Madabhushi, A., & Rusu, M. (2018). Fused Radiology-Pathology Lung (Lung-Fused-CT-Pathology) (Version 1) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/k9/tcia.2018.smt36lpn

Detailed Description

Supporting Documentation

The data set is fully described in the following publications:

Rusu et al. Co-registration of pre-operative CT with ex vivo surgically excised ground glass nodules to define spatial extent of invasive adenocarcinoma on in vivo imaging: a proof-of-concept study. European Radiology (2018); PMCID:PMC5630490 DOI:10.1007/s00330-017-4813-0

Histology Data Description

There is one folder for each patient, with the same folder name as the TCIA ID. Each folder with TCIA ID name contains 2 folders:

“images”
- Contains scanned histology images (in tiff format) pertinent to the TCIA ID Patient, e.g. LungFCP-01-0001_b1.tiff, LungFCP-01-0001_b2.tiff, etc
“annotations”
- Contains the pathologist’s annotations, stored as tiff file with the same image size as the scanned histology files, with 0 where there is not label, and 255 where a region was annotated. It is possible to have multiple annotations for each file, e.g. for file LungFCP-01-0001\images\LungFCP-01-0001_b1.tiff the following regions are available:
  - LungFCP-01-0001_b1_annotation_00_R000G255B000.tiff
  - LungFCP-01-0001_b1_annotation_00_R255G000B000.tiff

A part of the filenames (LungFCP-01-0001_b1_annotation_00_RxxxGyyyBzzz) indicate the type of annotation:

Adenocarcinoma in Situ : R000G000B255, R001G000B255, R002G000B255
Invasive Adenocarcinoma: R000G255B000, R001G255B000, R002G255B000, R003G255B000, R004G255B000, R005G255B000, R006G255B000
Invasive Adenocarcinoma + Adenocarcinoma in Situ: R255G000B000

If multiple files are available for the same type of annotation, e.g. Invasive Adenocarcinoma, it indicates that the pathologists has annotated multiple regions

Content of “FinalPublishedResults” folder

The folder “FinalPublishedResults” contains one folder for each patient. Within each patient folder, there are 3 subfolders: “CT”, ”Histology”, & ”Results_XX” where XX is a number. When expanded each patient folder appears as depicted below.

LungFCP-01-0001
- CT
  - CT.mha
    CT_crop_blood_label.mha
    CT_label_Meta_crop.mha
- histology
  - imgs
  - masks
    - blood
    - invasive
    - lesion
    - sample
    - (airways)
- Results_XX
  - blood_label.mha
    blood_label_up.mha
    blood_label_up_bin.mha
    invasion_label.mha
    invasion_label_up.mha
    invasion_label_up_bin.mha
    labels_up_bin.mha
    lesion.mha
    lesion_label.mha
    lesion_label_up.mha
    lesion_label_up_bin.mha
    reconstruction_grayscale.mha
    sample_label.mha
LungFCP-01-0002
LungFCP-01-0003
LungFCP-01-0004
LungFCP-01-0005
LungFCP-01-0006

The folder “CT” contains the 3D CT volume saved as one mha file, the segmentation of the lesion obtained by majority voting for the three radiologist segmentations, and the segmentation of the blood vessels.

The folder “histology” has a similar content as the raw histology data, but a lower resolution, with some additional processing, e.g. applied gross rotation and flipping to correct for artifacts related to the mounting on the glass slide, and with additional annotations beside the lesion and in situ disease, e.g. blood vessels.

The folder Results_XX contain the outcome of the registration of the histopathology images and the CT.

All scripts used for generating these results are available at https://github.com/mirabelarusu/RadPathFusionLung

Please refer to the following publication for the methodological details:

Rusu M., Rajiah P., Gilkeson R., Yang M., Donatelli C., Thawani R., Jacono F.J., Linden P., Madabushi A. (2017) Co-registration of pre-operative CT with ex vivo surgically excised ground glass nodules to define spatial extent of invasive adenocarcinoma on in vivo imaging: a proof-of-concept study. European Radiology 27:10, 4209:4217. DOI: https://doi.org/10.1007/s00330-017-4813-0

Other Publications Using this Data

TCIA maintains a list of publications which leverage our data. If you have a publication you’d like to add, please contact TCIA’s Helpdesk.

Publication Citation

Rusu, M., Rajiah, P., Gilkeson, R., Yang, M., Donatelli, C., Thawani, R., Jacono, F. J., Linden, P., & Madabhushi, A. (2018) Co-registration of pre-operative CT with ex vivo surgically excised ground glass nodules to define spatial extent of invasive adenocarcinoma on in vivo imaging: a proof-of-concept study. European Radiology (Vol. 27, Issue 10, pp. 4209–4217). PMCID:PMC5630490 DOI: https://doi.org/10.1007/s00330-017-4813-0

TCIA Citation

Clark, K., Vendt, B., Smith, K., Freymann, J., Kirby, J., Koppel, P., Moore, S., Phillips, S., Maffitt, D., Pringle, M., Tarbox, L., & Prior, F. (2013). The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository. In Journal of Digital Imaging (Vol. 26, Issue 6, pp. 1045–1057). Springer Science and Business Media LLC. https://doi.org/10.1007/s10278-013-9622-7

LUNG-FUSED-CT-PATHOLOGY