Journal: Scientific Reports

Article Title: Fluorescence microscopy tensor imaging representations for large-scale dataset analysis

doi: 10.1038/s41598-020-62233-2

Figure Lengend Snippet: Heart microvasculature acquisition. 3D rendering of a representative volume of lectin-TRITC stained heart microvasculature. Comparison between the raw data ( a ) and the ML-based segmentation results ( b ). ( c , d ) Automated feature extraction of the vascular skeleton (red lines) with endpoints and bifurcations represented as nodes (green circles). Bounding box, 105 × 120 × 345 μm. ( e–g ) 3D rendering of a representative short-axis basal slice with fluorescence microvasculature signal ( e ), microvascular skeleton ( f ) and nodes ( g ). ( h–j ) 3D rendering of a representative sagittal slice with corresponding microvascular skeleton and node representations. Scale bars, 500 μm.

Article Snippet: For in vivo microvasculature labeling, mice were anesthetized with 1.5–2% isoflurane supplemented with oxygen prior to intravenous injection of Rhodamine-labelled Griffonia simplicifolia lectin (100 μl; RL-1102, Vector Laboratories, Burlingame, CA, USA).

Techniques: Staining, Comparison, Extraction, Fluorescence

Journal: Scientific Reports

Article Title: Fluorescence microscopy tensor imaging representations for large-scale dataset analysis

doi: 10.1038/s41598-020-62233-2

Figure Lengend Snippet: Covariance matrix and tensor imaging representation. 3D renderings of a representative volume of lectin-TRITC stained heart. ( a ) Image processed fluorescence data, ( b ) corresponding skeleton (white) and graph nodes (red), ( c ) nodes (white circles) and their connecting segments (white lines). Bounding box, 250 × 205 × 340 μm. ( d ) 3D representation of the covariance ellipsoid. All feature descriptors (segments, for the microvasculature case) present within the red sampling volume ε (corresponding to a voxel in the final 3D image) are plotted and rendered with a directionally encoded color, defined in the microscopy acquisition frame. ( e ) By calculating the covariance Cov of the vascular tracts we can obtain the entries of the variance-covariance matrix CM (3 × 3), which is a tensor of rank 2. Here the matrix’s diagonal entries are the variances, while the others are the covariances. ( f ) Image representation of the tensor field components of the mid axial plane of the representative volume of lectin-TRITC stained heart shown in (a), using a pseudo-color map. Off diagonal components rescaled for better contrast. ( g ) Rotating the reference frame makes it possible to diagonalize the CM tensor with the positive eigenvalues λ 1 , λ 2 , λ 3 related to the spread (variance) in the eigenvectors directions v 1 , v 2 , v 3 . ( h ) In the new principal axis frame, the principal eigenvector v 1 gives the main vascular directionality within every voxel. The square root of the eigenvalues is proportional to the ellipsoid radii. The eigenvectors to their orientations. ( i ) The 3D ellipsoid glyph-based visualization of the mid axial plane of the representative volume of lectin-TRITC stained heart shown in (a), describes the tensor information at any point along an axial plane of the microvasculature. Ellipsoid colors are rendered using a directional color-encoded map (X, red; Y, green; Z, blue). ( j ) 3D vector-field representation of the entire vascular volume in ( a ). ( k ) Voxel maps of the principal eigenvector component along the lab reference frame, using a pseudo-color map, for the mid axial plane of the representative volume of lectin-TRITC stained heart shown in (a). ( l ) Directional color-encoded maps of the CM eigenvectors for the same mid axial plane shown in (k). RGB components are defined as the absolute values of the eigenvectors’ XYZ components (see inset). Scale bars in ( f , k , l ), 50 μm.

Article Snippet: For in vivo microvasculature labeling, mice were anesthetized with 1.5–2% isoflurane supplemented with oxygen prior to intravenous injection of Rhodamine-labelled Griffonia simplicifolia lectin (100 μl; RL-1102, Vector Laboratories, Burlingame, CA, USA).

Techniques: Imaging, Staining, Fluorescence, Sampling, Microscopy, Plasmid Preparation

Journal: Scientific Reports

Article Title: Fluorescence microscopy tensor imaging representations for large-scale dataset analysis

doi: 10.1038/s41598-020-62233-2

Figure Lengend Snippet: Content visualization and vascular tractography. All representations and visualizations refer to the representative volume of lectin-TRITC stained heart shown in Fig. . The 3D perspective ( a ), axial ( b ) and sagittal ( c ) vector field representations of the primary eigenvector clearly show the spatial preferential orientation of the microvascular network present in the tissue volume of Fig. . Vectors are color coded to represent orientation with respect to the XYZ lab frame. ( d ) Map of the principal eigenvector along a sagittal plane (Supplementary Fig. ) of the volume in ( a ). The intensity corresponds to the principal eigenvector’s length, with hedgehogs representing its direction in space at each point in the field. ( e ) Ellipsoid glyph representation of the tensor field for the same sagittal plane. Different streamline groups represent different trajectories along the principal eigenvector direction. ( f ) Color-coded fiber tracts represent seeded streamlines along the principal eigenvector and illustrate the main distribution and direction of the microvasculature. 3D perspective ( g ), axial ( h ) and sagittal ( i ) vascular tractograms with an associated axial ellipsoid glyph representation. ( j–l ) Tomographic vascular tractograms obtained along the principal ( j ), secondary ( k ) and tertiary ( l ) eigenvector, respectively. 3D rendering of the vascular skeleton ( m ) and the segments connecting the graph nodes. Color coded, RGB . Bounding box, 250 × 205 × 340 μm. Scale bars, 50 μm.

Article Snippet: For in vivo microvasculature labeling, mice were anesthetized with 1.5–2% isoflurane supplemented with oxygen prior to intravenous injection of Rhodamine-labelled Griffonia simplicifolia lectin (100 μl; RL-1102, Vector Laboratories, Burlingame, CA, USA).

Techniques: Staining, Plasmid Preparation

Journal: Scientific Reports

Article Title: Fluorescence microscopy tensor imaging representations for large-scale dataset analysis

doi: 10.1038/s41598-020-62233-2

Figure Lengend Snippet: Tomographic vascular tractograms. (a-l) Representations and visualizations of the microvasculature for a lectin-TRITC stained apical short-axis slice (as shown in Fig. ). ( a ) Tomographic vector field representation of the vascular directional primary eigenvector in a lectin-TRITC stained apical short-axis slice (as shown in Fig. and plane 1 of Fig. S13). Tomographic vascular tractogram determined along the primary eigenvector ( b ) and magnified view of the posterior left/right ventricle border area ( c ). Scale bar, 100 μm. ( d ) 3D ellipsoid glyph representation of the tensor field for the representative slice in ( a ). ( e , f ) Tomographic vascular tractograms determined along the secondary ( e ) and tertiary ( f ) eigenvectors. ( g ) Skeleton axial view representation of the vascular network. ( h–l ) 3D magnified views of the area α To ( g ). Glyph tensor field representation ( h ) and vascular skeleton ( i ) with corresponding vector field representations ( j , k ). In ( j ) colors encode directional information, while in ( k ) a cold-hot pseudo-color map encodes the principal eigenvector projection’s magnitude along the vertical axis. ( l ) 3D rendering of the fiber tracts corresponding to the magnified area. ( m ) Tomographic directional vascular tractogram in a lectin-TRITC stained basal short-axis slice (plane 3 of Fig. S13). ( n , o ) Magnified skeleton representation of the microvasculature in λ and corresponding tractogram. ( p , q ) Skeleton representation of the microvasculature and corresponding tractogram for a representative lectin-TRITC stained sagittal slice (as shown in Fig. S1h). Scale bar, 500 μm.

Article Snippet: For in vivo microvasculature labeling, mice were anesthetized with 1.5–2% isoflurane supplemented with oxygen prior to intravenous injection of Rhodamine-labelled Griffonia simplicifolia lectin (100 μl; RL-1102, Vector Laboratories, Burlingame, CA, USA).

Techniques: Staining, Plasmid Preparation