Journal: Journal of the American Heart Association: Cardiovascular and Cerebrovascular Disease

Article Title: Dietary Branched‐Chain Amino Acids Modify Postinfarct Cardiac Remodeling and Function in the Murine Heart

doi: 10.1161/JAHA.124.037637

Figure Lengend Snippet: Examination of cardiac collagen content and organization: A , Intact midpapillary sections stained with PSR; B , quantification of PSR signal (cardiac fibrosis) and ( C ) scar thickness (n=6–9 biological replicates); D , Computational assessment of scar collagen architecture in SHG‐imaged infarct segments. Left to right, representative master SHG images from postinfarct scar regions (region of interest: 256×256 pixel), CurveAlign‐generated images displaying the spatial distribution (red dots) and direction (green lines) of collagen fiber segments, corresponding CurveAlign sourced heatmaps depicting the relative alignment of collagen fibers across the region (red denotes regions of high alignment), and, lastly, CT‐FIRE extracted fibers overlaid on master SHG images (individual fibers are separated by varying colored lines). From these computational analyses, macrostructural collagen attributes were enumerated and graphed, including ( E ) fiber alignment, ( F ) fiber width, and ( G ) fiber straightness (n=3 biological replicates per sex per group). Data are mean±SEM. Normality was assessed via Shapiro–Wilk test. Parametric unpaired Student's t test or nonparametric Mann–Whitney U test as appropriate. Scale bar=8.14 μm. BCAA indicates branched‐chain amino acid; PSR, picrosirius red; and SHG, second harmonic generation.

Article Snippet: The regions of interest were subject to computational analyses using MATLAB software packages CurveAlign and CT‐FIRE, as described, to quantify macrostructural attributes of the collagen fiber network (collagen fiber alignment, width, and straightness).

Techniques: Staining, Generated, MANN-WHITNEY

Journal: Methods in molecular biology (Clifton, N.J.)

Article Title: Methods for Quantifying Fibrillar Collagen Alignment

doi: 10.1007/978-1-4939-7113-8_28

Figure Lengend Snippet: An example of using CT-FIRE mode without the boundary mode of CurveAlign for both full image and ROI analyses in pancreatic tissue. The top row shows the SHG image from different types of pancreatic tissue. The middle row shows the CT-FIRE extracted fibers highlighted by different colored lines for the purpose of contrast, which are overlaid upon the SHG image. The bottom row is the “Overlay” image generated by CurveAlign showing the location (red dots) and orientation (green lines) of the extracted fibers as well as the annotated ROI overlaid upon the SHG image. The quantification of the full image and the representative ROI are displayed in the format of “mean orientation/alignment” at the top left corner of the middle row and bottom row, respectively. Both full image-based and ROI-based quantifications show that collagen fibers are more aligned in malignant ducts (Grade 1–3) than in normal and benign ducts. Default parameters were used here. Image size is 1024 × 1024 pixels, and ROI size is 256 × 256 pixels. The scale bar at the top left column indicates 50 μm, and all images are shown at the same scale

Article Snippet: Software Download the MATLAB Runtime Compiler (MCR) and the CurveAlign software from [ 36 ] and follow the detailed requirements and installation instructions from the above web page.

Techniques: Generated

Journal: Methods in molecular biology (Clifton, N.J.)

Article Title: Methods for Quantifying Fibrillar Collagen Alignment

doi: 10.1007/978-1-4939-7113-8_28

Figure Lengend Snippet: An example of using CurveAlign to quantify relative angle and ROI-based alignment on breast cancer tissue microarray. The first column shows the SHG image (in yellow) overlaid on the bright-field H&E image with four rectangular ROI annotations (in yellow) (top), the orientations and locations of extracted fibers using CT-FIRE mode (in green color) with four ROI annotations (in magenta) overlaid on the SHG image (in gray) (middle), and four rectangular ROI annotations (in yellow) overlaid on the SHG image (in gray) (bottom), respectively. The remaining four columns from left to right show the cropped images of the four ROIs, where for the ones in the top row, ROI name as well as its mean relative angle and ROI-based alignment in the format of “ROI name: mean relative angle/ROI alignment.” In the middle row, the blue line is used to associate the center of fiber extracted by CT-FIRE with the corresponding boundary locations, and the red line shows the fibers located either beyond the distance range or within the boundary. In the bottom row, the locations and orientations of fiber segments analyzed by CFR mode were indicated by red dots and green lines. From the figure, we can see that fibers in ROI 1 and ROI 3 are both well aligned, but there are more fibers in ROI 3 that are more perpendicularly aligned with respect to the tumor boundary. The boundary creation parameter is the same as in Fig. 6, i.e., pixel per micron ratio was set to 2; fiber extraction in CT-FIRE used default settings; the distance parameter was set to 250 pixels; the fraction of kept curvelets is set to 0.06. The image size is 2048 × 2048 pixels, and the sizes of ROI are identically set to 128 × 128 pixels. The scale bar for the full size image at the first column of the first row indicates 100 μm, scale bar for the ROI image at the second column of the first row indicates 25 μm, and all images either full size images or ROIs are shown at the same scale

Article Snippet: Software Download the MATLAB Runtime Compiler (MCR) and the CurveAlign software from [ 36 ] and follow the detailed requirements and installation instructions from the above web page.

Techniques: Microarray, Extraction

Journal: Methods in molecular biology (Clifton, N.J.)

Article Title: Methods for Quantifying Fibrillar Collagen Alignment

doi: 10.1007/978-1-4939-7113-8_28

Figure Lengend Snippet: Schematic workflow of quantifying collagen alignment using CurveAlign for a single image. For the images in step 4, the fiber location and orientation were highlighted by red dots and green lines, respectively; the red lines indicate the fibers are out of the interested region. For [4B], there are two types of ROI analysis, type 1 ([4Ba]) can directly run CFR mode on the annotated ROI, but type 2 [4Bb] needs to run a full image analysis first either in CFR mode or in CT-FIRE mode. CTF, CT-FIRE; CFR, curvelets fiber representation; BD, with boundary; no BD, without boundary; FULL, full image analysis; and ROI, ROI analysis. The scale bar shown in the image at the top middle column indicates 50 μm, and all images are shown at the same scale

Article Snippet: Software Download the MATLAB Runtime Compiler (MCR) and the CurveAlign software from [ 36 ] and follow the detailed requirements and installation instructions from the above web page.

Techniques:

Journal: Methods in molecular biology (Clifton, N.J.)

Article Title: Methods for Quantifying Fibrillar Collagen Alignment

doi: 10.1007/978-1-4939-7113-8_28

Figure Lengend Snippet: Graphical user interface of CurveAlign (a) and CT-FIRE (b)

Article Snippet: Software Download the MATLAB Runtime Compiler (MCR) and the CurveAlign software from [ 36 ] and follow the detailed requirements and installation instructions from the above web page.

Techniques:

Journal: Methods in molecular biology (Clifton, N.J.)

Article Title: Methods for Quantifying Fibrillar Collagen Alignment

doi: 10.1007/978-1-4939-7113-8_28

Figure Lengend Snippet: Two fiber analysis modes in CurveAlign: (a) representative curvelets used in CFR mode; (b) extracted individual fibers used in CT-FIRE. This image of a relatively low-resolution portion of a breast tissue microarray illustrates the ability of the CurveAlign platform to extract fibers even when the fibers are relatively low signal to noise ratio but also demonstrates the difference between the two modes in fiber extraction. In (a), the red dots show the fiber location and green lines show the orientation. In (b), extracted fibers are displayed in different colored lines. CFR mode (a) indicates the most prominent fibers but does not provide individual fiber extraction as in CT-FIRE mode (b), which instead provides the information for entire fibers. CFR mode missed some fibers in the region annotated in red ellipse in (a) where fibers have relative lower intensity values. For the fiber analysis here, all parameters were kept as default ones except that, in CFR mode, the fraction of kept curvelet was set to 0.06. The image size is 512 pixels x 512 pixels. The scale bar at the upper left corner of (a) indicates 50 μm, and all images are shown at the same scale

Article Snippet: Software Download the MATLAB Runtime Compiler (MCR) and the CurveAlign software from [ 36 ] and follow the detailed requirements and installation instructions from the above web page.

Techniques: Microarray, Extraction

Journal: Methods in molecular biology (Clifton, N.J.)

Article Title: Methods for Quantifying Fibrillar Collagen Alignment

doi: 10.1007/978-1-4939-7113-8_28

Figure Lengend Snippet: Demonstration of typical outputs of CurveAlign: (1) The top row shows the relative angle (with respect to a boundary) using fibers extracted in CT-FIRE mode, the left column of this row shows that the blue line is used to associate the center of the fiber extracted by CT-FIRE with the corresponding boundary location, and the red line is used to show the fibers located either beyond the distance range or within the boundary; the heatmap at the middle column uses red color to indicate larger relative angles, and the histogram at the right column shows the distribution of the relative angle of fibers within the range of 0 to 90°; (2) the middle row shows the angle (with respect to the horizontal) measurement with CFR mode, and the left column of this row uses a red dot to indicate the center of fiber segments and a green line to indicate the fiber orientation at that point; the heatmap at the middle column uses red color to indicate well aligned fiber regions, and the histogram at the right column shows the distribution of the angles within the range of 0 to 180°; and (3) the bottom row shows ROI analysis based on the result from the CFR results shown in the middle row. Two magenta rectangular ROIs are annotated on the SHG image at the first column of this row, the histograms of angles within these two ROIs are displayed at the middle and right columns. Both the mean angle and alignment coefficient are listed below each histogram except that alignment is not calculated based on the relative angle data. The boundaries were cropped from the mask image shown in Fig. 6; fiber extraction in CT-FIRE used default settings; the distance parameter was set to 250 pixels; the fraction of kept curvelets is set to 0.06, the image size is 512 × 512 pixels, and the sizes of ROI are identically set to 128 × 128 pixels. The scale bar at the upper left corner of the top row indicates 50 μm, and all images are shown at the same scale

Article Snippet: Software Download the MATLAB Runtime Compiler (MCR) and the CurveAlign software from [ 36 ] and follow the detailed requirements and installation instructions from the above web page.

Techniques: Extraction