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

Publications by the Dataset Authors

The authors recommended this paper as the best source of additional information about this dataset:

• 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

No publications by dataset authors were found.

Research Community Publications

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.