2611 scanned prostate biopsies from 460 patient cases sampled between 2015 and 2018. Annotation of clinical metadata and treatment decisions made in connection with biopsy sampling exist on case-level. Roughly 35% of the biopsies contain cancer. In-image annotations exists in macro images the form of ink markings from the clinical workflow.
Keywords: Prostate Cancer, Pathology.
Sample images
Sample images with reduced image quality. Please click to preview.
Dataset information
| Short name | SPROB20 |
|---|---|
| Origin | Clinical |
| Cite as | Peter Walhagen, Pontus Röbeck, Ewert Bengtsson, Christer Busch, and Michael Häggman (2020) Spear Prostate Biopsy 2020 (SPROB20) doi:10.23698/aida/sprob20 |
| Field | Pathology |
| Organ |
Prostate |
| Age span | 39 - 79 years, median 67 years |
| Title | Spear Prostate Biopsy 2020 (SPROB20) |
| Author |
Peter Walhagen
Pontus Röbeck Ewert Bengtsson Christer Busch Michael Häggman |
| Year | 2020 |
| DOI | doi:10.23698/aida/sprob20 |
| Status | Completed |
| Version | 1.0.0 |
| Scans | 2611 |
| Annotations | |
| Size | 492.6GB |
| Resolution | 0.2204 microns per pixel (40x) |
| Modality |
SM
|
| Scanner |
Hamamatsu NanoZoomer S60 |
| Stain | H&E |
| Phase | |
| References |
|
| Copyright | Copyright 2020 Michael Häggman, Uppsala University Hospital |
| Access |
Available under the following licenses, described in the License section below.
Controlled access
AIDA BY license
|
Annotation
The cases are annotated with clinical data relevant for the treatment decision and the following treatment decision made in conjunction with the biopsy sampling. Each image is given an identifier which can be connected to the case by the case mapping file. Clinical data and treatment decisions have been extracted by manual medical records search. The information about treatment is what has been noted in conjunction with the diagnosis. Some cases contain missing data in some of the fields as the data wasn’t available. Some of the biopsies are resliced versions of another biopsy belonging to the same case. Together with the images macro-images of the biopsies exist with localized annotation of gleason grade and cancer detection as provided in the clinical workflow.
Kernels
Example jupyter notebook, SPROB20_sample.ipynb, for loading data from the dataset is available at
https://github.com/spearpoint-analytics/sprob20
File formats
Images: Pyramidal .tif
Metadata: .csv
License
Controlled access
Free for use in legal and ethical medical diagnostics research. Please contact the dataset provider for terms of access.
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cc: michael.haggman@akademiska.se,aida-data@nbis.se
Subject: Requesting access to dataset doi:10.23698/aida/sprob20
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AIDA BY license
Copyright 2020 Michael Häggman, Uppsala University Hospital
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:
Peter Walhagen, Pontus Röbeck, Ewert Bengtsson, Christer Busch, and Michael Häggman (2020) Spear Prostate Biopsy 2020 (SPROB20) doi:10.23698/aida/sprob20.
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.