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Abstract
Multimodal imaging is a powerful strategy for combining information from multiple images. It involves several fields in the acquisition, processing and interpretation of images. As multimodal imaging is a vast subject area with various combinations of imaging techniques, it has been extensively reviewed. Here we focus on Matrix-assisted Laser Desorption Ionization Mass Spectrometry Imaging (MALDI-MSI) coupling other imaging modalities in multimodal approaches. While MALDI-MS images convey a substantial amount of chemical information, they are not readily informative about the morphological nature of the tissue. By providing a supplementary modality, MALDI-MS images can be more informative and better reflect the nature of the tissue. In this mini review, we emphasize the analytical and computational strategies to address multimodal MALDI-MSI.
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Chateigner-Boutin AL, Alvarado C, Devaux MF, Durand S, Foucat L, Geairon A, Grélard F, Jamme F, Rogniaux H, Saulnier L, Guillon F. The endosperm cavity of wheat grains contains a highly hydrated gel of arabinoxylan. Plant Sci 2021; 306:110845. [PMID: 33775355 DOI: 10.1016/j.plantsci.2021.110845] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 06/12/2023]
Abstract
Cereal grains provide a substantial part of the calories for humans and animals. The main quality determinants of grains are polysaccharides (mainly starch but also dietary fibers such as arabinoxylans, mixed-linkage glucans) and proteins synthesized and accumulated during grain development in a specialized storage tissue: the endosperm. In this study, the composition of a structure localized at the interface of the vascular tissues of the maternal plant and the seed endosperm was investigated. This structure is contained in the endosperm cavity where water and nutrients are transferred to support grain filling. While studying the wheat grain development, the cavity content was found to autofluoresce under UV light excitation. Combining multispectral analysis, Fourier-Transform infrared spectroscopy, immunolabeling and laser-dissection coupled with wet chemistry, we identified in the cavity arabinoxylans and hydroxycinnamic acids. The cavity content forms a "gel" in the developing grain, which persists in dry mature grain and during subsequent imbibition. Microscopic magnetic resonance imaging revealed that the gel is highly hydrated. Our results suggest that arabinoxylans are synthesized by the nucellar epidermis, released in the cavity where they form a highly hydrated gel which might contribute to regulate grain hydration.
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Affiliation(s)
| | | | | | | | - Loïc Foucat
- INRAE, UR BIA, F-44316, Nantes, France; INRAE, BIBS Facility, F-44316, Nantes, France
| | | | - Florent Grélard
- INRAE, UR BIA, F-44316, Nantes, France; INRAE, BIBS Facility, F-44316, Nantes, France
| | - Frédéric Jamme
- DISCO Beamline, SOLEIL Synchrotron, 91192, Gif-sur-Yvette, France
| | - Hélène Rogniaux
- INRAE, UR BIA, F-44316, Nantes, France; INRAE, BIBS Facility, F-44316, Nantes, France
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Grélard F, Legland D, Fanuel M, Arnaud B, Foucat L, Rogniaux H. Esmraldi: efficient methods for the fusion of mass spectrometry and magnetic resonance images. BMC Bioinformatics 2021; 22:56. [PMID: 33557761 PMCID: PMC7869484 DOI: 10.1186/s12859-020-03954-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/30/2020] [Indexed: 11/29/2022] Open
Abstract
Background Mass spectrometry imaging (MSI) is a family of acquisition techniques producing images of the distribution of molecules in a sample, without any prior tagging of the molecules. This makes it a very interesting technique for exploratory research. However, the images are difficult to analyze because the enclosed data has high dimensionality, and their content does not necessarily reflect the shape of the object of interest. Conversely, magnetic resonance imaging (MRI) scans reflect the anatomy of the tissue. MRI also provides complementary information to MSI, such as the content and distribution of water. Results We propose a new workflow to merge the information from 2D MALDI–MSI and MRI images. Our workflow can be applied to large MSI datasets in a limited amount of time. Moreover, the workflow is fully automated and based on deterministic methods which ensures the reproducibility of the results. Our methods were evaluated and compared with state-of-the-art methods. Results show that the images are combined precisely and in a time-efficient manner. Conclusion Our workflow reveals molecules which co-localize with water in biological images. It can be applied on any MSI and MRI datasets which satisfy a few conditions: same regions of the shape enclosed in the images and similar intensity distributions.
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Affiliation(s)
- Florent Grélard
- UR BIA, INRAE, 44316, Nantes, France. .,BIBS Facility, INRAE, 44316, Nantes, France.
| | - David Legland
- UR BIA, INRAE, 44316, Nantes, France.,BIBS Facility, INRAE, 44316, Nantes, France
| | - Mathieu Fanuel
- UR BIA, INRAE, 44316, Nantes, France.,BIBS Facility, INRAE, 44316, Nantes, France
| | - Bastien Arnaud
- UR BIA, INRAE, 44316, Nantes, France.,BIBS Facility, INRAE, 44316, Nantes, France
| | - Loïc Foucat
- UR BIA, INRAE, 44316, Nantes, France.,BIBS Facility, INRAE, 44316, Nantes, France
| | - Hélène Rogniaux
- UR BIA, INRAE, 44316, Nantes, France.,BIBS Facility, INRAE, 44316, Nantes, France
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Grélard F, Baldacci F, Vialard A, Domenger JP. New methods for the geometrical analysis of tubular organs. Med Image Anal 2017; 42:89-101. [PMID: 28780175 DOI: 10.1016/j.media.2017.07.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 06/08/2017] [Accepted: 07/27/2017] [Indexed: 11/28/2022]
Abstract
This paper presents new methods to study the shape of tubular organs. Determining precise cross-sections is of major importance to perform geometrical measurements, such as diameter, wall-thickness estimation or area measurement. Our first contribution is a robust method to estimate orthogonal planes based on the Voronoi Covariance Measure. Our method is not relying on a curve-skeleton computation beforehand. This means our orthogonal plane estimator can be used either on the skeleton or on the volume. Another important step towards tubular organ characterization is achieved through curve-skeletonization, as skeletons allow to compare two tubular organs, and to perform virtual endoscopy. Our second contribution is dedicated to correcting common defects of the skeleton by new pruning and recentering methods. Finally, we propose a new method for curve-skeleton extraction. Various results are shown on different types of segmented tubular organs, such as neurons, airway-tree and blood vessels.
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Affiliation(s)
- Florent Grélard
- Univ. Bordeaux, LaBRI, UMR 5800, F-33400 Talence, France; CNRS, LaBRI, UMR 5800, F-33400 Talence, France.
| | - Fabien Baldacci
- Univ. Bordeaux, LaBRI, UMR 5800, F-33400 Talence, France; CNRS, LaBRI, UMR 5800, F-33400 Talence, France
| | - Anne Vialard
- Univ. Bordeaux, LaBRI, UMR 5800, F-33400 Talence, France; CNRS, LaBRI, UMR 5800, F-33400 Talence, France
| | - Jean-Philippe Domenger
- Univ. Bordeaux, LaBRI, UMR 5800, F-33400 Talence, France; CNRS, LaBRI, UMR 5800, F-33400 Talence, France
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