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Dataset . 2024
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Data sources: Datacite
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Dataset . 2023
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Dataset . 2024
License: CC BY
Data sources: Datacite
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Dataset . 2024
License: CC BY
Data sources: Datacite
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Dataset . 2024
License: CC BY
Data sources: Datacite
ZENODO
Dataset . 2024
License: CC BY
Data sources: Datacite
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Image segmentations produced by BAMF under the AIMI Annotations initiative

Authors: Van Oss, Jeff; Murugesan, Gowtham Krishnan; McCrumb, Diana; Soni, Rahul;

Image segmentations produced by BAMF under the AIMI Annotations initiative

Abstract

The Imaging Data Commons (IDC)(https://imaging.datacommons.cancer.gov/) [1] connects researchers with publicly available cancer imaging data, often linked with other types of cancer data. Many of the collections have limited annotations due to the expense and effort required to create these manually. The increased capabilities of AI analysis of radiology images provides an opportunity to augment existing IDC collections with new annotation data. To further this goal, we trained several nnUNet [2] based models for a variety of radiology segmentation tasks from public datasets and used them to generate segmentations for IDC collections. To validate the models performance, roughly 10% of the predictions were manually reviewed and corrected by both a board certified radiologist and a medical student (non-expert). Additionally, this non-expert looked at all the ai predictions and rated them on a 5 point Likert scale . This record provides the AI segmentations, Manually corrected segmentations, and Manual scores for the inspected IDC Collection images. This work was done in two stages. Versions 1.x of this record were from the first stage. Versions 2.x added additional records. In the Version 2.x additions, the Likert scores were not reported by the manual reviewers. File Overview brain-mr.zip Segment Description: brain tumor regions: necrosis, edema, enhancing IDC Collection: UPENN-GBM Links: model weights, github breast-fdg-pet-ct.zip Segment Description: FDG-avid lesions in breast from FDG PET/CT scans QIN-Breast IDC Collection: QIN-Breast Links: model weights, github breast-mr.zip Segment Description: Breast, Fibroglandular tissue, structural tumor IDC Collection: duke-breast-cancer-mri Links: model weights, github kidney-ct.zip Segment Description: Kidney, Tumor, and Cysts from contrast enhanced CT scans IDS Collection: TCGA-KIRC, TCGA-KIRP, TCGA-KICH, CPTAC-CCRCC Links: model weights, github liver-ct.zip Segment Description: Liver from CT scans IDC Collection: TCGA-LIHC Links: model weights, github liver2-ct.zip Segment Description: Liver and Lesions from CT scans IDC Collection: HCC-TACE-SEG, COLORECTAL-LIVER-METASTASES Links: model weights, github liver-mr.zip Segment Description: Liver from T1 MRI scans IDC Collection: TCGA-LIHC Links: model weights, github lung-ct.zip Segment Description: Lung and Nodules (3mm-30mm) from CT scans IDC Collections: Anti-PD-1-Lung LUNG-PET-CT-Dx NSCLC Radiogenomics RIDER Lung PET-CT TCGA-LUAD TCGA-LUSC Links: model weights 1, model weights 2, github lung2-ct.zip Improved model version Segment Description: Lung and Nodules (3mm-30mm) from CT scans IDC Collections: QIN-LUNG-CT, SPIE-AAPM Lung CT Challenge Links: model weights, github lung-fdg-pet-ct.zip Segment Description: Lungs and FDG-avid lesions in the lung from FDG PET/CT scans IDC Collections: ACRIN-NSCLC-FDG-PET Anti-PD-1-Lung LUNG-PET-CT-Dx NSCLC Radiogenomics RIDER Lung PET-CT TCGA-LUAD TCGA-LUSC Links: model weights, github prostate-mr.zip Segment Description: Prostate from T2 MRI scans IDC Collection: ProstateX, Prostate-MRI-US-Biopsy Links: model weights, github Likert Score Definition: 5 Strongly Agree - Use-as-is (i.e., clinically acceptable, and could be used for treatment without change) 4 Agree - Minor edits that are not necessary. Stylistic differences, but not clinically important. The current segmentation is acceptable 3 Neither agree nor disagree - Minor edits that are necessary. Minor edits are those that the review judges can be made in less time than starting from scratch or are expected to have minimal effect on treatment outcome 2 Disagree - Major edits. This category indicates that the necessary edit is required to ensure correctness, and sufficiently significant that user would prefer to start from the scratch 1 Strongly disagree - Unusable. This category indicates that the quality of the automatic annotations is so bad that they are unusable. Zip File Folder Structure Each zip file in the collection correlates to a specific segmentation task. The common folder structure is ai-segmentations-dcm This directory contains the AI model predictions in DICOM-SEG format for all analyzed IDC collection files qa-segmentations-dcm This directory contains manual corrected segmentation files, based on the AI prediction, in DICOM-SEG format. Only a fraction, ~10%, of the AI predictions were corrected. Corrections were performed by radiologist (rad*) and non-experts (ne*) qa-results.csv CSV file linking the study/series UIDs with the ai segmentation file, radiologist corrected segmentation file, radiologist ratings of AI performance.

Keywords

segmentation, cancer, artificial intelligence, DICOM, radiology

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
2
Average
Average
Average
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Cancer Research