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  • A new 2.5 D representation for lymph node detection in CT (CT Lymph Nodes)

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changes.mady.by.user Brenda Fevrier-Sullivan

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changes.mady.by.user Justin Kirby

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The collection is aimed at the medical image computing community for developing and assessing computer-aided detection methods. Automated detection of lymph nodes can be an important clinical diagnostic tool but is very challenging due to the low contrast of surrounding structures in CT and to their varying sizes, poses, shapes and sparsely distributed locations. This data set is made available to make direct comparison to other detection methods in order to advance the state of the art.

Acknowledgements

  • We would like to acknowledge the individuals and institutions that have provided data for this collection:

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  • National Institutes of Health, Bethesda MD.   Special thanks to Dr. Holger R. Roth and Dr. Ronald Summers, Imaging Biomarkers and Computer-Aided Diagnosis Laboratory , Grant Magnuson Clinical Center .
  • Conversion of the segmentations into DICOM SEG representation was completed by Cosmin Ciausu using dcmqi (https://github.com/QIICR/dcmqi), assisted by Andrey Fedorov, David Clunie, and other members of the NCI Imaging Data Commons team. NCI Imaging Data Commons consortium is supported by the contract number 19X037Q from Leidos Biomedical Research under Task Order HHSN26100071 under Contract No. HHSN261201500003l from NCI.


Localtab Group


Localtab
activetrue
titleData Access

Data Access


Data TypeDownload all or Query/FilterLicense
Images, Segmentations (DICOM, 58.4 GB)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/19726546/TCIA_CT_Lymph_Nodes_03-31-2023.tcia?api=v2



Tcia button generator
labelSearch
urlhttps://www.cancerimagingarchive.net/nbia-search/?CollectionCriteria=CT%20Lymph%20Nodes



(Download requires the NBIA Data Retriever)

Tcia cc by 3

Med ABD Lymph Annotations (ZIP)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/19726546/MED_ABD_LYMPH_ANNOTATIONS.zip?version=1&modificationDate=1435166807156&api=v2



Tcia cc by 3

Med Lymph Candidate Nodes (ZIP)


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urlhttps://wiki.cancerimagingarchive.net/download/attachments/19726546/MED_ABD_LYMPH_CANDIDATES.zip?version=1&modificationDate=1442245247654&api=v2



Tcia cc by 3

Med ABD Lymph Masks ( ZIP)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/19726546/MED_ABD_LYMPH_MASKS.zip?version=1&modificationDate=1449684916503&api=v2



Tcia cc by 3


Click the Versions tab for more info about data releases.

Nci_crdc additional resources




Localtab
titleDetailed Description

Detailed Description


Collection Statistics


Modalities

CT, SEG

Number of Participants

176

Number of Studies

176

Number of Series

352

Number of Images

110,179

Images Size (GB)

58.4


The DICOM files were created from volumetric images (Analyze and NifTI) using this from ITK:   http://www.itk.org/Doxygen/html/Examples_2IO_2ImageReadDicomSeriesWrite_8cxx-example.html.

Annotation files

  MED_ABD_LYMPH_ANNOTATIONS.zip  (new 6/24/2015). The annotations include a folder for each case with text files of voxel indices, physical coordinates, size measurements and a MITK point set file (.mps), which can be visualized using the MITK workbench (Note: only release 2014.10.0 and later supports visualization of point set files using the "point set interaction plugin"). Abdominal size measurements include the longest and shortest axis in axial view of a lymph node. The shortest axis is used for the RECIST criteria. The mediastinal set only includes the shortest axis.

Mediastinal and abdominal lymph nodes

Computer-generated candidate detections for mediastinal and abdominal lymph nodes (produced by methods in [K. Cherry et al., SPIE Med. Img. 2014] and [J. Liu et al., SPIE Med. Img. 2014]]).  See attached: MED_ABD_LYMPH_CANDIDATES.zip (new 9/14/2015).

MED_ABD_LYMPH_MASKS.zip  (new 12/8/2015): These files contain a compressed NifTI image (*.nii.gz) for each patient with manually traced lymph node segmentations. Note: these segmentation masks were produced independently to the centroid annotations in MED_ABD_LYMPH_ANNOTATIONS.zip. There is an overlapping set of lymph nodes marked in both files but the indexing does not align.  On 3/31/2023 (version 5) a DICOM-SEG version of these data were added to the collection.

Please cite the following paper when using the segmentation masks:

A Seff, L Lu, A Barbu, H Roth, HC Shin, RM Summers. Leveraging Mid-Level Semantic Boundary Cues for Automated Lymph Node Detection. Medical Image Computing and Computer-Assisted Intervention–MICCAI 2015, 53-61 (http://link.springer.com/chapter/10.1007/978-3-319-24571-3_7)




Localtab
titleCitations & Data Usage Policy

Citations & Data Usage Policy 

Tcia limited license policy

Info
titleData Citation

Roth, H., Lu, L., Seff, A., Cherry, K. M., Hoffman, J., Wang, S., Liu, J., Turkbey, E., & Summers, R. M. (2015). A new 2.5 D representation for lymph node detection in CT [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2015.AQIIDCNM


Info
titlePublication Citation

Roth, H. R., Lu, L., Seff, A., Cherry, K. M., Hoffman, J., Wang, S., Liu, J., Turkbey, E., & Summers, R. M. (2014). A New 2.5D Representation for Lymph Node Detection Using Random Sets of Deep Convolutional Neural Network Observations. In Medical Image Computing and Computer-Assisted Intervention – MICCAI 2014 (pp. 520–527). Springer International Publishing. https://doi.org/10.1007/978-3-319-10404-1_65


Info
titlePublication Citation

Seff, A., Lu, L., Cherry, K.M., Roth, H.R., Liu, J., Wang, S., Hoffman, J., Turkbey, E.B., & Summers, R.M. 2D view aggregation for lymph node detection using a shallow hierarchy of linear classifiers. Medical Image Computing and Computer-Assisted Intervention--MICCAI 2014, p544-552, 2014. (http://arxiv.org/abs/1408.3337)


Info
titlePublication Citation

Please cite the following paper when using the segmentation masks:

Seff, A., Lu, L., Barbu, A., Roth, H., Shin, H.-C., & Summers, R. M. (2015). Leveraging Mid-Level Semantic Boundary Cues for Automated Lymph Node Detection. In Lecture Notes in Computer Science Medical Image Computing and Computer-Assisted Intervention–MICCAI 2015 (pp. 53–61). Springer International Publishing. https://doi.org/10.1007/978-3-319-24571-3_7



Info
titleTCIA 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. Journal of Digital Imaging, 26(6), 1045–1057. https://doi.org/10.1007/s10278-013-9622-7


Other Publications Using This Data

TCIA maintains a list of publications that leverage our data. At this time we are not aware of any publications based on this data. If you have a publication you'd like to add please contact the TCIA Helpdesk.




Localtab
titleVersions

Version 5 (Current): Updated 2023/03/31


Data TypeDownload all or Query/Filter
Image, Segmentations (DICOM, 58.4 GB)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/19726546/TCIA_CT_Lymph_Nodes_03-31-2023.tcia?api=v2



Tcia button generator
labelSearch
urlhttps://www.cancerimagingarchive.net/nbia-search/?CollectionCriteria=CT%20Lymph%20Nodes



(Download requires the NBIA Data Retriever)

Med ABD Lymph Annotations (ZIP)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/19726546/MED_ABD_LYMPH_ANNOTATIONS.zip?version=1&modificationDate=1435166807156&api=v2



Med Lymph Candidate Nodes (ZIP)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/19726546/MED_ABD_LYMPH_CANDIDATES.zip?version=1&modificationDate=1442245247654&api=v2



Med ABD Lymph Masks (ZIP)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/19726546/MED_ABD_LYMPH_MASKS.zip?version=1&modificationDate=1449684916503&api=v2



Added DICOM version of MED_ABD_LYMPH_MASKS.zip segmentations that were previously available

Version 4 : Updated 2015/12/14


Data TypeDownload all or Query/Filter
Images (DICOM, 57.8GB)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/19726546/TCIA_CT_Lymph_Nodes_06-22-2015.tcia?version=1&modificationDate=1534787005035&api=v2



Tcia button generator
labelSearch
urlhttps://www.cancerimagingarchive.net/nbia-search/?CollectionCriteria=CT%20Lymph%20Nodes



(Download requires the NBIA Data Retriever)

Med ABD Lymph Annotations (ZIP)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/19726546/MED_ABD_LYMPH_ANNOTATIONS.zip?version=1&modificationDate=1435166807156&api=v2



Med Lymph Candidate Nodes (ZIP)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/19726546/MED_ABD_LYMPH_CANDIDATES.zip?version=1&modificationDate=1442245247654&api=v2



Med ABD Lymph Masks (ZIP)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/19726546/MED_ABD_LYMPH_MASKS.zip?version=1&modificationDate=1449684916503&api=v2




MED_ABD_LYMPH_MASKS.zip added via the wiki.

Version 3: Updated 2015/09/14

MED_ABD_LYMPH_CANDIDATES.zip  added via the wiki.

Version 2: Updated 2015/06/24

  MED_ABD_LYMPH_ANNOTATIONS.zip   added via the wiki.

Version 1: Updated 2015/03/16

Image data set uploaded




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