| 1. |
- Hedlund, Joel, 1978-, et al.
(författare)
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Key insights in the AIDA community policy on sharing of clinical imaging data for research in Sweden
- 2020
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Ingår i: Scientific Data. - : Springer Nature. - 2052-4463. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Development of world-class artificial intelligence (AI) for medical imaging requires access to massive amounts of training data from clinical sources, but effective data sharing is often hindered by uncertainty regarding data protection. We describe an initiative to reduce this uncertainty through a policy describing a national community consensus on sound data sharing practices.
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| 2. |
- Zhang, Zhixin, et al.
(författare)
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Vectorized rooftop area data for 90 cities in China
- 2022
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Ingår i: Scientific Data. - : Springer Nature. - 2052-4463. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- Reliable information on building rooftops is crucial for utilizing limited urban space effectively. In recent decades, the demand for accurate and up-to-date data on the areas of rooftops on a large-scale is increasing. However, obtaining these data is challenging due to the limited capability of conventional computer vision methods and the high cost of 3D modeling involving aerial photogrammetry. In this study, a geospatial artificial intelligence framework is presented to obtain data for rooftops using high-resolution open-access remote sensing imagery. This framework is used to generate vectorized data for rooftops in 90 cities in China. The data was validated on test samples of 180 km(2) across different regions with spatial resolution, overall accuracy, and F1 score of 1 m, 97.95%, and 83.11%, respectively. In addition, the generated rooftop area conforms to the urban morphological characteristics and reflects urbanization level. These results demonstrate that the generated dataset can be used for data support and decision-making that can facilitate sustainable urban development effectively.
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| 3. |
- Akbar, Muhammad Usman, 1990-, et al.
(författare)
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Brain tumor segmentation using synthetic MR images - A comparison of GANs and diffusion models
- 2024
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Ingår i: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Large annotated datasets are required for training deep learning models, but in medical imaging data sharing is often complicated due to ethics, anonymization and data protection legislation. Generative AI models, such as generative adversarial networks (GANs) and diffusion models, can today produce very realistic synthetic images, and can potentially facilitate data sharing. However, in order to share synthetic medical images it must first be demonstrated that they can be used for training different networks with acceptable performance. Here, we therefore comprehensively evaluate four GANs (progressive GAN, StyleGAN 1–3) and a diffusion model for the task of brain tumor segmentation (using two segmentation networks, U-Net and a Swin transformer). Our results show that segmentation networks trained on synthetic images reach Dice scores that are 80%–90% of Dice scores when training with real images, but that memorization of the training images can be a problem for diffusion models if the original dataset is too small. Our conclusion is that sharing synthetic medical images is a viable option to sharing real images, but that further work is required. The trained generative models and the generated synthetic images are shared on AIDA data hub.
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| 4. |
- Buetti-Dinh, Antoine, 1984-, et al.
(författare)
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Systems biology of acidophile biofilms for efficient metal extraction
- 2020
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Ingår i: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 7:1, s. 1-10
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Tidskriftsartikel (refereegranskat)abstract
- Society's demand for metals is ever increasing while stocks of high-grade minerals are being depleted. Biomining, for example of chalcopyrite for copper recovery, is a more sustainable biotechnological process that exploits the capacity of acidophilic microbes to catalyze solid metal sulfide dissolution to soluble metal sulfates. A key early stage in biomining is cell attachment and biofilm formation on the mineral surface that results in elevated mineral oxidation rates. Industrial biomining of chalcopyrite is typically carried out in large scale heaps that suffer from the downsides of slow and poor metal recoveries. In an effort to mitigate these drawbacks, this study investigated planktonic and biofilm cells of acidophilic (optimal growth pH < 3) biomining bacteria. RNA and proteins were extracted, and high throughput "omics" performed from a total of 80 biomining experiments. In addition, micrographs of biofilm formation on the chalcopyrite mineral surface over time were generated from eight separate experiments. The dataset generated in this project will be of great use to microbiologists, biotechnologists, and industrial researchers.
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| 5. |
- Buga, Roxana M., et al.
(författare)
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HISTOBREAST : a collection of brightfield microscopy images of Haematoxylin and Eosin stained breast tissue
- 2020
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Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- Modern histopathology workflows rely on the digitization of histology slides. The quality of the resulting digital representations, in the form of histology slide image mosaics, depends on various specific acquisition conditions and on the image processing steps that underlie the generation of the final mosaic, e.g. registration and blending of the contained image tiles. We introduce HISTOBREAST, an extensive collection of brightfield microscopy images that we collected in a principled manner under different acquisition conditions on Haematoxylin - Eosin (H&E) stained breast tissue. HISTOBREAST is comprised of neighbour image tiles and ensemble of mosaics composed from different combinations of the available image tiles, exhibiting progressively degraded quality levels. HISTOBREAST can be used to benchmark image processing and computer vision techniques with respect to their robustness to image modifications specific to brightfield microscopy of H&E stained tissues. Furthermore, HISTOBREAST can serve in the development of new image processing methods, with the purpose of ensuring robustness to typical image artefacts that raise interpretation problems for expert histopathologists and affect the results of computerized image analysis.
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| 6. |
- Malesevic, Nebojsa, et al.
(författare)
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A database of multi-channel intramuscular electromyogram signals during isometric hand muscles contractions
- 2020
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Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- Hand movement is controlled by a large number of muscles acting on multiple joints in the hand and forearm. In a forearm amputee the control of a hand prosthesis is traditionally depending on electromyography from the remaining forearm muscles. Technical improvements have made it possible to safely and routinely implant electrodes inside the muscles and record high-quality signals from individual muscles. In this study, we present a database of intramuscular EMG signals recorded with fine-wire electrodes alongside recordings of hand forces in an isometric setup and with the addition of spike-sorted metadata. Six forearm muscles were recorded from twelve able-bodied subjects and nine forearm muscles from two subjects. The fully automated recording protocol, based on command cues, comprised a variety of hand movements, including some requiring slowly increasing/decreasing force. The recorded data can be used to develop and test algorithms for control of a prosthetic hand. Assessment of the signals was done in both quantitative and qualitative manners.
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| 7. |
- Mota, A, et al.
(författare)
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Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH
- 2022
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Ingår i: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 9:1, s. 47-
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Tidskriftsartikel (refereegranskat)abstract
- Single-molecule DNA fluorescence in situ hybridization (FISH) techniques enable studying the three-dimensional (3D) organization of the genome at the single cell level. However, there is a major unmet need for open access, high quality, curated and reproducible DNA FISH datasets. Here, we describe a dataset obtained by applying our recently developed iFISH method to simultaneously visualize 16 small (size range: 62–73 kilobases, kb) DNA loci evenly spaced on chromosome 2 in human cells, in a single round of hybridization. We show how combinatorial color coding can be used to precisely localize multiple loci in 3D within single cells, and how inter-locus distances scale inversely with chromosome contact frequencies determined by high-throughput chromosome conformation capture (Hi-C). We provide raw images and 3D coordinates for nearly 10,000 FISH dots. Our dataset provides a free resource that can facilitate studies of 3D genome organization in single cells and can be used to develop automatic FISH analysis algorithms.
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| 8. |
- Orlecka-Sikora, Beata, et al.
(författare)
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An open data infrastructure for the study of anthropogenic hazards linked to georesource exploitation
- 2020
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Ingår i: Scientific Data. - : Springer. - 2052-4463. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Mining, water-reservoir impoundment, underground gas storage, geothermal energy exploitation and hydrocarbon extraction have the potential to cause rock deformation and earthquakes, which may be hazardous for people, infrastructure and the environment. Restricted access to data constitutes a barrier to assessing and mitigating the associated hazards. Thematic Core Service Anthropogenic Hazards (TCS AH) of the European Plate Observing System (EPOS) provides a novel e-research infrastructure. The core of this infrastructure, the IS-EPOS Platform (tcs.ah-epos.eu) connected to international data storage nodes offers open access to large grouped datasets (here termed episodes), comprising geoscientific and associated data from industrial activity along with a large set of embedded applications for their efficient data processing, analysis and visualization. The novel team-working features of the IS-EPOS Platform facilitate collaborative and interdisciplinary scientific research, public understanding of science, citizen science applications, knowledge dissemination, data-informed policy-making and the teaching of anthropogenic hazards related to georesource exploitation. TCS AH is one of 10 thematic core services forming EPOS, a solid earth science European Research Infrastructure Consortium (ERIC) (www.epos-ip.org).
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| 9. |
- Schweiker, Marcel, et al.
(författare)
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The Scales Project, a cross-national dataset on the interpretation of thermal perception scales
- 2019
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Ingår i: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- Thermal discomfort is one of the main triggers for occupants' interactions with components of the built environment such as adjustments of thermostats and/or opening windows and strongly related to the energy use in buildings. Understanding causes for thermal (dis-)comfort is crucial for design and operation of any type of building. The assessment of human thermal perception through rating scales, for example in post-occupancy studies, has been applied for several decades; however, long-existing assumptions related to these rating scales had been questioned by several researchers. The aim of this study was to gain deeper knowledge on contextual influences on the interpretation of thermal perception scales and their verbal anchors by survey participants. A questionnaire was designed and consequently applied in 21 language versions. These surveys were conducted in 57 cities in 30 countries resulting in a dataset containing responses from 8225 participants. The database offers potential for further analysis in the areas of building design and operation, psycho-physical relationships between human perception and the built environment, and linguistic analyses.
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| 10. |
- Schäfer, Michael, et al.
(författare)
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DOES : A multimodal dataset for supervised and unsupervised analysis of steel scrap
- 2023
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Ingår i: Scientific Data. - : Nature Research. - 2052-4463. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- DOES - Dataset of European scrap classes. Today, scrap is already an important raw material for industry. Due to the transformation to green steel, the secondary raw material scrap will become increasingly important in the coming years. With DOES a free dataset is presented, which represents common non-alloyed European scrap classes. Two important points were considered in this dataset. First, scrap oxidizes under normal external conditions and the visual appearance changes, which plays an important role in visual inspections. Therefore, DOES includes scrap images of different degrees of corrosion attack. Second, images of scrap metal (mostly scrap piles) usually have no intrinsic order. For this reason, a technique to extract many overlapping rectangles from raw images was used, which can be used to train deep learning algorithms without any disadvantage. This dataset is very suitable to develop industrial applications or to research classification algorithms. The dataset was validated by experts and through machine learning models.
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