A preclinical micro-computed tomography database including 3D whole body organ segmentations.
Stefanie RosenhainZuzanna A MagnuskaGrace G YamoahWa'el Al RawashdehFabian KießlingFelix GremsePublished in: Scientific data (2018)
The gold-standard of preclinical micro-computed tomography (μCT) data processing is still manual delineation of complete organs or regions by specialists. However, this method is time-consuming, error-prone, has limited reproducibility, and therefore is not suitable for large-scale data analysis. Unfortunately, robust and accurate automated whole body segmentation algorithms are still missing. In this publication, we introduce a database containing 225 murine 3D whole body μCT scans along with manual organ segmentation of most important organs including heart, liver, lung, trachea, spleen, kidneys, stomach, intestine, bladder, thigh muscle, bone, as well as subcutaneous tumors. The database includes native and contrast-enhanced, regarding spleen and liver, μCT data. All scans along with organ segmentation are freely accessible at the online repository Figshare. We encourage researchers to reuse the provided data to evaluate and improve methods and algorithms for accurate automated organ segmentation which may reduce manual segmentation effort, increase reproducibility, and even reduce the number of required laboratory animals by reducing a source of variability and having access to a reliable reference group.
Keyphrases
- deep learning
- contrast enhanced
- computed tomography
- dual energy
- data analysis
- convolutional neural network
- diffusion weighted
- magnetic resonance imaging
- positron emission tomography
- machine learning
- artificial intelligence
- image quality
- magnetic resonance
- electronic health record
- big data
- diffusion weighted imaging
- adverse drug
- cell therapy
- social media
- heart failure
- healthcare
- high resolution
- skeletal muscle
- atrial fibrillation
- stem cells
- high throughput
- soft tissue
- bone mineral density
- mesenchymal stem cells
- emergency department
- postmenopausal women
- pet ct