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Place figure a bit later
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iarganda authored Sep 22, 2022
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* **‘Verbose’**: show all the steps performed by the script in the form of text inside the ImageJ/Fiji Log window.

## Tables of results and output information

| ![Example of output files generated by the 'folded' script](./images/documentation/Output-files-example.jpg) |
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| **Figure S3: Example of output files generated by the 'folded' script.** |

The script generates a folder for each analyzed image (here exemplified as ```‘ImageFileName’```) containing the following image files:
* ```‘ImageFileName_binary.tif’```: the binarized version of the input image used for the skeletonization process and the enamel thickness analysis (Figure 2D-F).
* ```‘ImageFileName_coherency.tif’```: a grayscale image showing the values resulting from the enamel folding analysis. Lighter colors represent more folded areas (note in the Figure 2G is shown with an inverse pattern for visualization purposes).
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* ```‘ImageFileName_thickness.tif’```: a grayscale image with the result of the LocalThickness plugin (Figure 2F).
* ```‘ImageFileName_kmeans.tif’```: an RGB color image with the results of the k-means algorithm and the 2D orientation patch count (Figure 2I).

| ![Example of output files generated by the 'folded' script](./images/documentation/Output-files-example.jpg) |
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| **Figure S3: Example of output files generated by the 'folded' script.** |

In addition, a series of data tables in csv format are generated. Some of them include pixel-by-pixel values, useful for intra-tooth analyses, and a summary file ```‘ImageFileName_summary.csv’``` with all the information from that specific specimen compiled). The list of tables is as follows:
* ```‘ImageFileName_complexity.csv’```: a comma-separated data table with the number of skeleton (equivalent to each region of interest, ROI), branch (subdivision of each ROI), X, Y, and Z coordinates, enamel folding values (‘Folding’), location within the ROI (‘Distance by ROI’) and distance within the linear enamel length (‘Accumulated distance’).
* ```‘ImageFileName_dentine.csv’```: a comma-separated data table with the area and perimeter in both pixels2 and the selected measuring unit2 of the dentine.
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