Whole slide pathology images from regional lymph node metastasis in colon adenocarcinoma produced at Region Gävleborg Clinical Pathology and Cytology department and Region Östergötland Clinical Pathology department. Annotations for AI training produced as part of AIDA clinical fellowship project investigating AI decision support in metastasis detection.

This dataset has been extended with a second collection series in the LNCO2 dataset using different collection and annotation parameters.

Keywords: Pathology, Whole slide imaging, Annotated, Lymph nodes, Cancer, Colon, Adenocarcinoma.

Sample images

Sample images with reduced image quality. Please click to preview.

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Dataset information

Short name	LNCO
Origin	Clinical
Cite as	Gordan Maras, Martin Lindvall, and Claes Lundstrom (2019) Regional lymph node metastasis in colon adenocarcinoma doi:10.23698/aida/lnco [BibTeX format] @misc{ maras_2019_lnco, author = { Gordan Maras and Martin Lindvall and Claes Lundstrom }, title = { Regional lymph node metastasis in colon adenocarcinoma }, year = 2019, publisher = { AIDA }, doi = { 10.23698/aida/lnco }, howpublished = { Available: AIDA Data Hub }, url = { https://datahub.aida.scilifelab.se/10.23698/aida/lnco } }
Field	Pathology
Organ	Colon
Age span
Title	Regional lymph node metastasis in colon adenocarcinoma
Author	Gordan Maras Martin Lindvall Claes Lundstrom
Year	2019
DOI	doi:10.23698/aida/lnco
Status	Completed
Version	1.2.0
Scans	977
Annotations	7379
Size	373.66GB
Resolution	20x and 40x
Modality	SM
Scanner	Aperio Scanscope (20x) Hamamatsu NanoZoomer (40x)
Stain	Hematoxylin and eosin.
Phase
References
Copyright	Copyright 2019 Linköping University, Claes Lundström
Access	Available under the following licenses, described in the License section below. Controlled access Free for use in legal and ethical medical diagnostics research. AIDA BY license Free for use within AIDA with attribution.

Annotation

ROI boxes around lymph nodes (positive, negative or unasssed) and detailed tumor polygons

See details below.

Annotation details

Labels

The following labels exists:

• roi_lgl_norm:: Region contains a lymph node section that do not contain tumor-positive areas, eg, is normal or negative. (but see also note below)

• roi_lgl_unknown:: Region contains a lymph node for which ground truth has not been established.

• roi_lgl_tumor:: Region contains a lymph node where at least some areas are tumor-positive areas. (Might not be annotated)

• roi_lgl_exclude:: Contains lymph node that was determined to be of poor quality or contain severe artifacts from scanning. Would be excluded from clinial review (not suitable).

• tumor:: region exclusively contains tumor pixels (but see also excl category below)

• excl & excl_artifact:: these areas should be substracted from tumor-annotated regions to gain pure-tumor pixels.

• bkg: region contains only background pixels

NOTE: tumor annotations are not exhaustive, meaning, there might be more tumor areas in lgl_roi_tumor lymph nodes than annotated with tumor annotations.

NOTE: Some roi_lgl_norm areas contain tumor cells that are from an accidental contamination of the glass during processing. This is normal during routine clinical work and a challenge that automated systems should deal with in an appropriate manner. This is a very easy task for human pathologists to discern.

NOTE: tumor regions not within a roi_lgl_* region should be assumed to be annotations of tumor in the the primary tumor. This can easily be verified visually, and the primary tumor is always on the initial blocks of the case (A..B…C etc)

Sampling procedure

Sampling procedure: Query for patients with confirmed adenocarcinomas that underwent colorectomy with subsequent lymphnode review as part of TNM-staging. Query selected N cases with a relatively high number of reported positive lymph nodes.

Source: Two medical clinics in Sweden.

Descriptive statistics

LNCO1
  patients: 39
  cases: 39
  images: 977
     median dimensions(WxH px): 49799 x 38729
     median resolution (micrometer per pixel): 0.4959
  annotations:
    number: 7379
    lymph node sections (roi) 1557
      which are negative 712
      which are positive 292
      which are unassessed 525
    images with at least one detailed tumor annotation: 165

File formats

Pixel position scaling

Coordinates given are relative to the image width. To get the correct pixel position, X coordinates (and Y coordinates!) should therefore be multiplied with the image width.

License

Controlled access

Free for use in legal and ethical medical diagnostics research. Please contact the dataset provider for terms of access.

You are invited to send an access request email from your institutional account.

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To: claes.lundstrom@liu.se
cc: gordan.maras@regiongavleborg.se,aida-data@nbis.se
Subject: Requesting access to dataset doi:10.23698/aida/lnco
Hi!

I work at INSTITUTION in COUNTRY, emailing from my institutional account.

I would like to access the dataset doi:10.23698/aida/lnco, for use in ethical and legal medical diagnostics research. Could you please send me a data sharing agreement template?

Our planned use of the data can be summarized as:

BRIEF_DESCRIPTION_OF_PLANNED_ACTIVITIES

Dataset: https://datahub.aida.scilifelab.se/10.23698/aida/lnco

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AIDA BY license

Copyright 2019 Linköping University, Claes Lundström

Permission to use, copy, modify, and/or distribute this data within Analytic Imaging Diagnostics Arena (AIDA) for the purpose of medical diagnostics research with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies, and that publications resulting from the use of this data cite the following works:

Gordan Maras, Martin Lindvall, and Claes Lundstrom (2019) Regional lymph node metastasis in colon adenocarcinoma doi:10.23698/aida/lnco.

THE DATA IS PROVIDED “AS IS” AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS DATA INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR CHARACTERISTICS OF THIS DATA.