Dataset Information

A patch-based super resolution algorithm for improving image resolution in clinical mass spectrometry.

ABSTRACT: Mass spectrometry imaging (MSI) and histology are complementary analytical tools. Integration of the two imaging modalities can enhance the spatial resolution of the MSI beyond its experimental limits. Patch-based super resolution (PBSR) is a method where high spatial resolution features from one image modality guide the reconstruction of a low resolution image from a second modality. The principle of PBSR lies in image redundancy and aims at finding similar pixels in the neighborhood of a central pixel that are then used to guide reconstruction of the central pixel. In this work, we employed PBSR to increase the resolution of MSI. We validated the proposed pipeline by using a phantom image (micro-dissected logo within a tissue) and mouse cerebellum samples. We compared the performance of the PBSR with other well-known methods: linear interpolation (LI) and image fusion (IF). Quantitative and qualitative assessment showed advantage over the former and comparability with the latter. Furthermore, we demonstrated the potential applicability of PBSR in a clinical setting by accurately integrating structural (i.e., histological) and molecular (i.e., MSI) information from a case study of a dog liver.

SUBMITTER: Scupakova K

PROVIDER: S-EPMC6393664 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

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A patch-based super resolution algorithm for improving image resolution in clinical mass spectrometry.

Ščupáková Klára K Terzopoulos Vasilis V Jain Saurabh S Smeets Dirk D Heeren Ron M A RMA

Scientific reports 20190227 1

Mass spectrometry imaging (MSI) and histology are complementary analytical tools. Integration of the two imaging modalities can enhance the spatial resolution of the MSI beyond its experimental limits. Patch-based super resolution (PBSR) is a method where high spatial resolution features from one image modality guide the reconstruction of a low resolution image from a second modality. The principle of PBSR lies in image redundancy and aims at finding similar pixels in the neighborhood of a centr ...[more]

PMID: 30814528

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Project description:The disease spots on the grape leaves can be detected by using the image processing and deep learning methods. However, the accuracy and efficiency of the detection are still the challenges. The convolutional substrate information is fuzzy, and the detection results are not satisfactory if the disease spot is relatively small. In particular, the detection will be difficult if the number of pixels of the spot is <32 × 32 in the image. In order to effectively address this problem, we present a super-resolution image enhancement and convolutional neural network-based algorithm for the detection of black rot on grape leaves. First, the original image is up-sampled and enhanced with local details using the bilinear interpolation. As a result, the number of pixels in the image increase. Then, the enhanced images are fed into the proposed YOLOv3-SPP network for detection. In the proposed network, the IOU (Intersection Over Union, IOU) in the original YOLOv3 network is replaced with GIOU (Generalized Intersection Over Union, GIOU). In addition, we also add the SPP (Spatial Pyramid Pooling, SPP) module to improve the detection performance of the network. Finally, the official pre-trained weights of YOLOv3 are used for fast convergence. The test set test_pv from the Plant Village and the test set test_orchard from the orchard field were used to evaluate the network performance. The results of test_pv show that the grape leaf black rot is detected by the YOLOv3-SPP with 95.79% detection accuracy and 94.52% detector recall, which is a 5.94% greater in terms of accuracy and 10.67% greater in terms of recall as compared to the original YOLOv3. The results of test_orchard show that the method proposed in this paper can be applied in field environment with 86.69% detection precision and 82.27% detector recall, and the accuracy and recall were improved to 94.05 and 93.26% if the images with the simple background. Therefore, the detection method proposed in this work effectively solves the detection task of small targets and improves the detection effectiveness of the grape leaf black rot.

Dataset Information

A patch-based super resolution algorithm for improving image resolution in clinical mass spectrometry.

Publications

A patch-based super resolution algorithm for improving image resolution in clinical mass spectrometry.

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