Weakly supervised semantic segmentation for MRI: exploring the advantages and disadvantages of class activation maps for biological image segmentation with soft boundaries

publishedVersio

Diffusion tensor imaging for spatially-resolved characterization of muscle fiber structure in seafood

The fiber structure of tissue in meat and seafood has a significant impact on their perceived quality. However, quantifiable description of muscle structure is challenging. We investigate diffusion tensor imaging (DTI) magnetic resonance imaging (MRI) as a method to quantitatively describe tissue structure. DTI measures the anisotropy of water molecule diffusion within muscle fibers. A pilot study evaluated three different cod loin samples: one of high-quality, one of medium-quality, and one of poor-quality. DTI parameters such as fractional anisotropy, axial diffusion and radial diffusion showed clear differences between the sample qualities. Changes in the DTI metrics consistent with freezing and thawing damage to the tissue were observed. The DTI maps were compared to T2-weighted images and DTI detected significant details that were not visible in T2-weighted images. Overall, these results indicate that DTI is a promising method for spatially-resolved characterization of tissue structure in seafood and meat

Magnetic resonance imaging for non-invasive measurement of plastic ingestion in marine wildlife

Monitoring plastic ingestion by marine wildlife is important for both characterizing the extent of plastic pollution in the environment and understanding its effect on species and ecosystems. Current methods to detect plastic in the digestive system of animals are slow and invasive, such that the number of animals that can be screened is limited. In this article, magnetic resonance imaging (MRI) is investigated as a possible technology to perform rapid, non-invasive detection of plastic ingestion. Standard MRI methods were able to directly measure one type of plastic in a fulmar stomach and another type was able to be indirectly detected. In addition to MRI, other standard nuclear magnetic resonance (NMR) measurements were made. Different types of plastic were tested, and distinctive NMR signal characteristics were found in common for each type, allowing them to be distin- guished from one another. The NMR results indicate specialized MRI sequences could be used to directly image several types of plastic. Although current commercial MRI technology is not suitable for field use, existing single- sided MRI research systems could be adapted for use outside the laboratory and become an important tool for future monitoring of wild animals

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

Characterization of vasskveite (water halibut) syndrome for automated detection

In recent years, cases of vasskveite (water halibut) syndrome in halibut have been increasing. At the moment, there exists no way to screen for the syndrome immediately after capture, which is problematic for both exporters and purchasers. In this article, we compared good quality halibut and halibut exhibiting the syndrome using a variety of techniques. Hyperspectral imaging was used to quantify the relative amounts of fat and water in the tissue. Diffusion tensor imaging was used to characterize tissue structure. Histology was performed to provide direct visual characterization of the tissue. Results indicate the muscle fibers in afflicted fish exhibit disordered growth and the tissue is lacking in fat. These results are in line with the current theory that the syndrome stems from a nutritional deficiency in the halibut diet. Hyperspectral imaging appears to be a promising technology to rapidly identify afflicted halibut immediately after capture

Predicting liquid loss of frozen and thawed cod from hyperspectral imaging

publishedVersio

Online monitoring of enzymatic hydrolysis of marine by-products using benchtop nuclear magnetic resonance spectroscopy

Enzymatic hydrolysis is becoming a more commonly used method to create high value products from traditionally low value marine by-products. However, improvement to processing is hampered by a lack of ways to characterize the reaction in real time. Current methods of analysis rely on taking offline samples, deactivating the enzymes, and performing analysis on the products afterwards. Nuclear magnetic resonance benchtop spectroscopy was investigated as a method for online process monitoring of enzymatic hydrolysis. Online and offline NMR measurements were performed for enzymatic hydrolysis reactions on red cod, salmon and shrimp. Both the online and offline measurements were able to follow the reaction process and showed good agreement in their calculated reaction rate. Application of the methodology to several types of raw materials indicates the technique is robust with regards to sample type. Advantages and disadvantages of low-field versus high-field NMR spectroscopy are discussed as well as practical considerations needed in order to apply the method industrially.submittedVersio

Online monitoring of enzymatic hydrolysis of marine by-products using benchtop nuclear magnetic resonance spectroscopy

Enzymatic hydrolysis is becoming a more commonly used method to create high value products from traditionally low value marine by-products. However, improvement to processing is hampered by a lack of ways to characterize the reaction in real time. Current methods of analysis rely on taking offline samples, deactivating the enzymes, and performing analysis on the products afterwards. Nuclear magnetic resonance benchtop spectroscopy was investigated as a method for online process monitoring of enzymatic hydrolysis. Online and offline NMR measurements were performed for enzymatic hydrolysis reactions on red cod, salmon and shrimp. Both the online and offline measurements were able to follow the reaction process and showed good agreement in their calculated reaction rate. Application of the methodology to several types of raw materials indicates the technique is robust with regards to sample type. Advantages and disadvantages of low-field versus high-field NMR spectroscopy are discussed as well as practical considerations needed in order to apply the method industrially

Mechanisms of transverse relaxation of water in muscle tissue

Nuclear magnetic resonance (NMR), and in particular transverse relaxation (T2), has been used to characterize meat and seafood products for decades. Despite many years of research, it is still not possible to reproducibly correlate the transverse relaxation of muscle foods to attributes that determine their quality and value. Instead of directly trying to interpret the T2 spectrum itself, typically chemometrics is used to try to relate the relaxation distributions to other measured properties on the sample. As muscle tissue is a porous medium, it is tempting to use equations developed to analyze other porous systems to provide a more direct, quantitative description of the tissue. However, the standard equations used to characterize porous materials have been developed for predominantly geological systems. This article discusses the foundations of transverse relaxation theory in porous media and the challenges that arise when attempting to adapt the equations to a biological system like tissue. One of the biggest issues that needs to be overcome before porous media theory can be reliably applied to characterize meat and seafood is to determine the source of relaxivity in the tissue. In order to better understand how the NMR signal originates, T2, diffusion, T1-T2 correlation and T2-T2 exchange experiments were performed on Atlantic cod (Gadus morhua) tissue in a variety of states (e.g. fresh, thawed, homogenized, etc.). In the literature, typically four T2 peaks are reported for meat and seafood samples. Results of this study indicate that the fastest relaxation peak is attributable to hydrogen within the protein itself and therefore arises from dipolar coupling. The T2B peak appears to belong to a type of bound water in protein called “buried water”, and its relaxation stems from a combination of restricted motion and interaction with the hydrogen in the protein. For the T21 peak, attributed to fluid in myofibrils, the main relaxation mechanism is the interaction between water molecules and the hydrogen in myosin/actin matrix. The T22 peak arises predominantly from the interaction of water with dissolved protein in the sarcoplasm. An important finding from the study is the need to include both surface sinks and volume sinks in the interpretation of T2 relaxation results. Given these sources of the transverse relaxation in tissue, it is highly likely that changes to the T2 distribution that have been attributed to microstructural changes in the tissue are in reality due to a combination of changes in microstructure, surface relaxation and fluid properties. These findings aid in better interpreting T2 measurements in meat and seafood products and present a step towards a systematic approach for using transverse relaxation to quantitatively describe changes in tissue, with the ultimate aim of eventually predicting product quality and value from NMR relaxometry