Whole slide pathology images from regional lymph node metastasis in colon adenocarcinoma produced at Region Gävleborg Clinical Pathology and Cytology department. Consists of fifty chronologically consecutive cases.

This dataset represents a second collection series in connection to the LNCO dataset using different collection and annotation parameters.

Keywords: Pathology, Annotated, Whole slide imaging, 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	LNCO2
Origin	Clinical
Cite as	Gordan Maras, Martin Lindvall, and Claes Lundstrom (2020) Regional lymph node metastasis in colon adenocarcinoma, second collection series doi:10.23698/aida/lnco2
Field	Pathology
Organ	Colon
Age span
Title	Regional lymph node metastasis in colon adenocarcinoma, second collection series
Author	Gordan Maras Martin Lindvall Claes Lundstrom
Year	2020
DOI	doi:10.23698/aida/lnco2
Status	Completed
Version	1.2.0
Scans	1245
Annotations	2598
Size	651.76GB
Resolution	20x and 40x
Modality	SM
Scanner	Aperio Scanscope (20x) Hamamatsu NanoZoomer (40x)
Stain	Hematoxylin and eosin.
Phase
References
Copyright	Copyright 2020 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

Lymph nodes have been identified by an experienced pathologist and annotated using region-of-interest boxes (positive, negative, unassested). A few detailed polygons of tumor exist. 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).

• roi_tumor:: Region mostly contains positive pixels, but not guaranteed that all pixels are positive.

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

• bkg: region contains only background pixels

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

Sampling procedure

Sampling procedure: Query for patients with confirmed adenocarcinomas that underwent colorectomy with subsequent lymphnode review as part of TNM-staging. Selected 50 chronologically consecutive cases from unique patients (no patient has more than one case).

Source: One medical clinic in Sweden. Same as for LNCO1.

Descriptive statistics

LNCO2
  patients: 50
  cases: 50
  images: 1245
     median dimensions(WxH px): 49920 x 38016
     median resolution (micrometer per pixel): 0.459896982
  annotations:
    number: 2598
    lymph node sections (roi) 2551
      which are negative 948
      which are positive 75
      which are unassessed 1517
    images with at least one approximate tumor annotation: 30

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/lnco2
Hi!

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

I would like to access the dataset doi:10.23698/aida/lnco2, 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/lnco2

Example agreement template: https://datahub.aida.scilifelab.se/sharing/templates/

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AIDA BY license

Copyright 2020 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 (2020) Regional lymph node metastasis in colon adenocarcinoma, second collection series doi:10.23698/aida/lnco2.

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.