Clinical Image Data Sources: An Overview
This article contains an overview of Clinical Image Data Sources. Due to divers angels of clinical studies the data collected in these studies have various formats. This data variety provides different solutions for a lot of complex biological questions. However, the downside of this data variety is the complex data storage, processing and comparing. For every different data set new ways of storing and processing must be dealt with. This is a problem that can be hard to deal with, especially for intensive processing or deep learning tasks. In order to tackle these problems in the Genematics Cloud imaging project, we have set up a list of clinical data sources deemed useful or relevant to this project. For each source the license and availability has been checked. Moreover, every source on this list can be used for other projects, studies or data processing tasks, although individual restrictions may apply at specific sources.
Although, each source varies in data type, origin, size, focus of data and accessibility, the following topics have been reviewed for each data source:
Source: The name of the database, dataset or publisher.
Data Types: Types of images found in this source.
- XR: Plain Xray
- CT: CT scan
- MR: MRI scan
- US: Ultrasound
- PE: PET scan
Data Focus: The main focus of the dataset images in terms of body location or function.
Images: The amount of images in this data source.
Patients: The amount of patients that contributed to this data source.
Availability: The requirements for accessing this data source.
License: The license and restrictions for this data source.
Link: The Direct URL to the data source, apply form or website closest to the data source. Unknown values are annotated as X.
| Source | Data Type | Data Focus | Images | Patients | Availability | License | Link |
| Alzheimer’s Disease Neuroimaging Initiative (ADNI) | MR, PE | Brain | X | X | Request on application form | Non-commercial, non-modify, non-distribute | http://adni.loni.usc.edu/data-samples/access-data/ |
| AMRG Atlas | MR | Heart | 78 | 1 | Request on application form | Non-commercial, non-modify, non-distribute | http://www.cardiacatlas.org/studies/amrg-cardiac-atlas/ |
| Autism Brain Imaging Data Exchange (ABIDE) | MR | Brain | X | 539 | Registration | Non-commercial | http://preprocessed-connectomes-project.org/abide/ |
| Belarus Tuberculosis Portal | XR, CT | Lungs | X | 500+ | Open | Non-commercial | http://www.tuberculosis.by |
| CHD Atlas | MR | Heart | X | X | Request on application form | Non-commercial, non-modify, non-distribute | http://www.cardiacatlas.org/studies/chd-atlas/ |
| DETERMINE | MR | Heart | X | X | Request on application form | Non-commercial, non-modify, non-distribute | http://www.cardiacatlas.org/studies/determine/ |
| Digital Database for Screening Mammography (DDSM) | XR | All | X | 2620 | Open | Primarily research and algorithm development | http://marathon.csee.usf.edu/Mammography/Database.html |
| Digital Retinal Images for Vessel Extraction (DRIVE) | MR | Heart | X | 400 | Registration | Non-commercial, non-modify, non-distribute | https://www.isi.uu.nl/Research/Databases/DRIVE/download.php |
| Initiative for Collaborative Computer Vision Benchmarking (Prostate) | MR | Prostate | X | X | Open | MIT license | https://zenodo.org/record/162231#.Wg6gyGRaOUm |
| Japanese Society of Radiological Technology Database (JSRT) | CT | Lungs | 250+ | 250+ | Registration | Non-commercial, non-distribute | http://db.jsrt.or.jp/eng.php |
| MedPix | XR, CT, MR, US, PE | All | 53,000+ | 13,000+ | Registration | Personal use only, including local private distribution | https://medpix.nlm.nih.gov/home |
| Multi-Ethnic Study of Atherosclerosis | MR | Heart | X | 6,500+ | Registration | Non-commercial, non-modify, non-distribute | https://www.mesa-nhlbi.org |
| Montgomery County X-ray Set | MR | Lungs | 138 | X | Open | MIT license | https://ceb.nlm.nih.gov/repositories/tuberculosis-chest-x-ray-image-data-sets/ |
| Open Access Series of Imaging Series (OASIS) | MR | Brain | 373 | 186 | Registration | Modify and distribute on creator agreement | http://www.oasis-brains.org |
| Osirix DICOM Library | CT, MR, PE | All | X | X | Monthly subscription | Non-commercial, non-distribute | http://www.osirix-viewer.com/resources/dicom-image-library/ |
| SCMR Consensus Data | MR | All | 193¹ | 15 | Request on application form | Non-commercial, non-modify, non-distribute | http://www.cardiacatlas.org/studies/scmr-consensus-data/ |
| Shenzhen Chest X-ray Set | CT | Lungs | 662 | X | Open | MIT license | https://ceb.nlm.nih.gov/repositories/tuberculosis-chest-x-ray-image-data-sets/ |
| Sunnybrook Cardiac Data (SCD) | MR | Heart | X | 46 | Request on application form | Non-commercial, non-modify, non-distribute | http://www.cardiacatlas.org/studies/sunnybrook-cardiac-data/ |
| The cancer Imaging Archive (TCIA) | XR, CT, MR, US, PE | All | X | 40,000+ | Open | Non-modify, additional restrictions on specific sub datasets | http://www.cancerimagingarchive.net |
¹ Number of MRI slices
Feature image credit: Marcin Sadlowski. Licensed via Adobe Stock.