SAR imaging and detection of partially coherent targets

A synthetic aperture radar (SAR) achieves a high azimuth resolution by illuminating targets with multiple pulses and using the Doppler history to synthesize a large antenna. When combining the pulses, it is normally assumed that the targets are stationary, and that their reflectivity is independent of time. The topic of this thesis is the processing of SAR images where the the targets have a time-dependent reflectivity. One can imagine, for instance, a ship rolling in a rough sea. One possible way of processing such targets is described by R. Keith Raney. The goal of this thesis is to provide a well structured introduction into Raney's formalism on partially coherent targets, and to investigate a focusing strategy for scenes where the targets have different coherence times. The image formation processes of a synthetic aperture radar is thoroughly discussed, and a one-dimensional model of the azimuth dimension is introduced. Raney's formalism is compared to this model and found to be formally correct. A partially coherent point target is simulated, and Raney's formalism is tested for the purpose of target detection in the presence of scene partial coherence. It is shown that the whole system, including partial coherence in both scene and processor, behaves as a Gaussian low-pass filter weighted by the scene autocorrelation function and the processor coherence function

Early identification of mushy Halibut syndrome with hyperspectral image analysis

Mushy Halibut Syndrome (MHS) is a condition that appears in Greenland halibut and manifests itself as abnormally opaque, flaccid and jelly-like flesh. Fish affected by this syndrome show poor meat quality, which results in negative consequences for the fish industry. The research community has not carefully investigated this condition, nor novel technologies for MHS detection have been proposed. In this research work, we propose using hyperspectral imaging to detect MHS. After collecting a dataset of hyperspectral images of halibut affected by MHS, two different goals were targeted. Firstly, the estimation of the chemical composition of the samples (specifically fat and water content) from their spectral data by using constrained spectral unmixing. Secondly, supervised classification using partial least squares discriminant analysis (PLS-DA) was evaluated to identify specimens affected by MHS. The outcomes of our study suggest that the prediction of fat from the spectral data is possible, but the prediction of the water content was not found to be accurate. However, the detection of MHS using PLS-DA was precise for hyperspectral images from both fillets and whole fish, with lower bounds of 75% and 83% for precision and recall, respectively. Our findings suggest hyperspectral imaging as a suitable technology for the early screening of MHS.Early identification of mushy Halibut syndrome with hyperspectral image analysispublishedVersio

Early identification of mushy Halibut syndrome with hyperspectral image analysis

Mushy Halibut Syndrome (MHS) is a condition that appears in Greenland halibut and manifests itself as abnormally opaque, flaccid and jelly-like flesh. Fish affected by this syndrome show poor meat quality, which results in negative consequences for the fish industry. The research community has not carefully investigated this condition, nor novel technologies for MHS detection have been proposed. In this research work, we propose using hyperspectral imaging to detect MHS. After collecting a dataset of hyperspectral images of halibut affected by MHS, two different goals were targeted. Firstly, the estimation of the chemical composition of the samples (specifically fat and water content) from their spectral data by using constrained spectral unmixing. Secondly, supervised classification using partial least squares discriminant analysis (PLS-DA) was evaluated to identify specimens affected by MHS. The outcomes of our study suggest that the prediction of fat from the spectral data is possible, but the prediction of the water content was not found to be accurate. However, the detection of MHS using PLS-DA was precise for hyperspectral images from both fillets and whole fish, with lower bounds of 75% and 83% for precision and recall, respectively. Our findings suggest hyperspectral imaging as a suitable technology for the early screening of MHS.Early identification of mushy Halibut syndrome with hyperspectral image analysispublishedVersio

Perspective Chapter: Hyperspectral Imaging for the Analysis of Seafood

Hyperspectral imaging technology is able to provide useful information about the interaction between electromagnetic radiation and matter. This information makes possible chemical characterization of materials in a non-invasive manner. For this reason, the technology has been of great interest for the food industry in recent decades. In this book chapter, we provide a survey of the current status of the use of hyperspectral technology for seafood evaluation. First, we provide a brief description of the optical properties of tissue and an introduction to the instrumentation used to capture these images. Then, we survey the main applications of hyperspectral imaging in the seafood industry, including the quantification of different chemical components, the estimation of freshness, the quality assessment of seafood products, and the detection of nematodes, among others. Finally, we provide a discussion about the current state of the art and the upcoming challenges for the application of this technology in the seafood industry

Effect of the T90-codend on the catch quality of cod (Gadus morhua) compared to the conventional codend configuration in the Barents Sea bottom trawl fishery

The aim of this study was to compare the catch quality of Northeast Atlantic cod (Gadus morhua) in the Barents Sea bottom trawl fishery caught using the conventional configuration (a sorting grid followed by a diamond mesh (T0) codend) and a T90° turned mesh codend (T90) without a grid. Twenty hauls were conducted, consisting of 10 hauls with the conventional configuration and 10 hauls with the T90-codend. The catch quality was assessed using the catch-damages-index (CDI) and a newly developed method using VIS/NIR hyperspectral imaging to estimate the residual blood abundances in the fish muscle. The probability of obtaining fish with no damage was 23.4% (CI: 16.3–31.1%) for cod captured by the conventional configuration, and 21.2% (CI: 15.4–27.2%) for cod captured by the T90-codend. The average blood abundance (in arbitrary unit) was 0.86 (CI: 0.85–0.87) for cod captured by the conventional configuration and 0.88 (CI: 0.87–0.88) for cod captured by the T90-codend. Catch quality of the hauls obtained using the two gears did not differ significantly in terms of catch damage or residual blood levels in the cod. Hence, this study demonstrated that T90-codends do not compromise catch quality compared to regular diamond meshed codends.publishedVersio

Raman spectroscopy and NIR hyperspectral imaging for in-line estimation of fatty acid features in salmon fillets

Raman spectroscopy was compared with near infrared (NIR) hyperspectral imaging for determination of fat composition (%EPA + DHA) in salmon fillets at short exposure times. Fillets were measured in movement for both methods. Salmon were acquired from several different farming locations in Norway with different feeding regimes, representing a realistic variation of salmon in the market. For Raman, we investigated three manual scanning strategies; i) line scan of loin, ii) line scan of belly and iii) sinusoidal scan of belly at exposure times of 2s and 4s. NIR images were acquired while the fillets moved on a conveyor belt at 40 cm/s, which corresponds to an acquisition time of 1s for a 40 cm long fillet. For NIR images, three different regions of interest (ROI) were investigated including the i) whole fillet, ii) belly segment, and iii) loin segment. For both Raman and NIR measurements, we investigated an untrimmed and trimmed version of the fillets, both relevant for industrial in-line evaluation. For the trimmed fillets, a fat rich deposition layer in the belly was removed. The %EPA + DHA models were validated by cross validation (N = 51) and using an independent test set (N = 20) which was acquired in a different season. Both Raman and NIR showed promising results and high performances in the cross validation, with R2CV = 0.96 for Raman at 2s exposure and R2CV = 0.97 for NIR. High performances were obtained also for the test set, but while Raman had low and stable biases for the test set, the biases were high and varied for the NIR measurements. Analysis of variance on the squared test set residuals showed that performance for Raman measurements were significantly higher than NIR at 1% significance level (p = 0.000013) when slope-and-bias errors were not corrected, but not significant when residuals were slope-and-bias corrected (p = 0.28). This indicated that NIR was more sensitive to matrix effects. For Raman, signal-to-noise ratio was the main limitation and there were indications that Raman was close to a critical sample exposure time at the 2s signal accumulation.publishedVersio

Applications of hyperspectral imaging for documenting smoltification status and welfare in Atlantic salmon

publishedVersio

Digital phenotyping of individual feed intake in Atlantic salmon (Salmo salar) with the X-ray method and image analysis

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Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in selected cancer types have suggested that chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we analyze patterns of chromothripsis across 2,658 tumors from 38 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of more than 50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy-number states, a considerable fraction of events involve multiple chromosomes and additional structural alterations. In addition to non-homologous end joining, we detect signatures of replication-associated processes and templated insertions. Chromothripsis contributes to oncogene amplification and to inactivation of genes such as mismatch-repair-related genes. These findings show that chromothripsis is a major process that drives genome evolution in human cancer