Three ‐dimensional NMR microscopy of zebrafish specimens

High resolution MRM was used to image formalin ‐fixed and formalin‐fixed paraffin embedded zebrafish specimens to study morphology of the mutants. It is demonstrated that 3D images with resolution up to 25 μm/pixel with strong contrast (T1W, T2W, MT, DWI or their combinations) could be obtained. That enables (semi)automatic organ segmentati on. While zebrafish embryos in the first five days after fertilization are clear and amenable to optical analysis, older juveniles and adults are not, due to pigmentation development and tissue growth. Thus other imaging methods are needed to image adult specimens. NMR is a versatile tool for studies of biological systems and has been successfully used for in vivo zebrafish microscopy. In this work we use NMR microscopy (MRM) for assessment of zebrafish specimens, which includes imaging of formalin fixed (FF), formalin fixed and paraffin embedded (FFPE), fresh (unfixed), and FF gadolinium doped specimens. To delineate the size and shape of various organs we concentrated on 3D MRM. We have shown that at 7  T a 3D NMR image can be obtained with isotropic resolution of 50 μm/pxl within 10 min and 25 μm/pxl within 4 h. Also, we have analyzed sources of contrast and have found that in FF specimens the best contrast is obtained byT1 weighting (3D FLASH, 3D FISP), whereas in FFPE specimensT2 weighting (3D RARE) is the best. We highlight an approach to perform segmentation of the organs in order to study morphological changes associate...
Source: NMR in Biomedicine - Category: Radiology Authors: Tags: RESEARCH ARTICLE Source Type: research
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