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Data released on May 21, 2018

Supporting data for "1399 H&E-stained sentinel lymph node sections of breast cancer patients: the CAMELYON dataset"

Litjens, G; Bandi, P; Bejnordi, B, E; Geessink, O; Balkenhol, M; Bult, P; Halilovic, A; Hermsen, M; de Loo, R, V; Vogels, R; Manson, Q; Stathonikos, N; Baidoshvili, A; Diest, P, V; Wauters, C; Dijk, M, V; Laak, J, V (2018): Supporting data for "1399 H&E-stained sentinel lymph node sections of breast cancer patients: the CAMELYON dataset" GigaScience Database. http://dx.doi.org/10.5524/100439 RIS BibTeX Text

The presence of lymph node metastases is one of the most important factors in breast cancer prognosis. The most common strategy to assess the regional lymph node status is the sentinel lymph node procedure. The sentinel lymph node is the most likely lymph node to contain metastasized cancer cells and is excised, histopathologically processed and examined by the pathologist. This tedious examination process is time-consuming and can lead to small metastases being missed. However, recent advances in whole-slide imaging and machine learning have opened an avenue for analysis of digitized lymph node sections with computer algorithms. For example, convolutional neural networks, a type of machine learning algorithm, are able to automatically detect cancer metastases in lymph nodes with high accuracy. To train machine learning models, large, well-curated datasets are needed. We released a dataset of 1399 annotated whole-slide images of lymph nodes, both with and without metastases, in total three terabytes of data in the context of the CAMELYON16 and CAMELYON17 Grand Challenges. Slides were collected from five different medical centers to cover a broad range of image appearance and staining variations. Each whole-slide image has a slide-level label indicating whether it contains no metastases, macro-metastases, micro-metastases or isolated tumor cells. Furthermore, for 209 whole-slide images, detailed hand-drawn contours for all metastases are provided. Last, open-source software tools to visualize and interact with the data have been made available. A unique dataset of annotated, whole-slide digital histopathology images has been provided with high potential for re-use.

Contact Submitter

Additional information:

https://github.com/GeertLitjens/ASAP

Projects:



Keywords:

breast cancer lymph node metastases whole-slide images grand challenge sentinel node 

Imaging

http://gigadb.org/images/data/cropped/100439.png

Funding:

  • Funding body - Stichting IT Projecten
  • Funding body - Fonds Economische Structuurversterking
  • Comment - tEPIS/TRAIT project
  • Funding body - Fonds Economische Structuurversterking
  • Award ID - DFES1029161
  • Funding body - Fonds Economische Structuurversterking
  • Comment - LSH-FES Program 2009
  • Funding body - Fonds Economische Structuurversterking
  • Award ID - FES1103JJTBU
  • Funding body - European Union
  • Award ID - 601040
  • Comment - FP7-funded VPH-PRISM project

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
normal_0319606HumanhumanHomo sapiens Description:Histology images of lymph node used in...
Sex:female
Sample source:CAMELYON16
...
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normal_0329606HumanhumanHomo sapiens Description:Histology images of lymph node used in...
Sex:female
Sample source:CAMELYON16
...
+
normal_0339606HumanhumanHomo sapiens Description:Histology images of lymph node used in...
Sex:female
Sample source:CAMELYON16
...
+
normal_0349606HumanhumanHomo sapiens Description:Histology images of lymph node used in...
Sex:female
Sample source:CAMELYON16
...
+
normal_0359606HumanhumanHomo sapiens Description:Histology images of lymph node used in...
Sex:female
Sample source:CAMELYON16
...
+
normal_0369606HumanhumanHomo sapiens Description:Histology images of lymph node used in...
Sex:female
Sample source:CAMELYON16
...
+
normal_0379606HumanhumanHomo sapiens Description:Histology images of lymph node used in...
Sex:female
Sample source:CAMELYON16
...
+
normal_0389606HumanhumanHomo sapiens Description:Histology images of lymph node used in...
Sex:female
Sample source:CAMELYON16
...
+
normal_0399606HumanhumanHomo sapiens Description:Histology images of lymph node used in...
Sex:female
Sample source:CAMELYON16
...
+
normal_0409606HumanhumanHomo sapiens Description:Histology images of lymph node used in...
Sex:female
Sample source:CAMELYON16
...
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Displaying 31-40 of 599 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
Data Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDData TypeFile FormatSizeRelease Date 
GitHub archivearchive679.44 KB2018-05-16
ScriptUNKNOWN4.22 KB2018-05-16
Imagearchive714.99 KB2018-05-16
Scriptarchive5.22 KB2018-05-16
Scriptarchive3.08 KB2018-05-16
Imagearchive2.59 MB2018-05-16
Imagearchive7.34 MB2018-05-16
Imagearchive329.43 KB2018-05-16
normal_001ImageTIF1.17 GB2018-05-16
normal_002ImageTIF1.46 GB2018-05-16
Displaying 1-10 of 611 File(s).

History:

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