poreScanner v2.1

User manual Authors Vincenzo Giacalone, Civilini Vittoria, Alberto Audenino, Mara Terzini Software version v.2.1 License CC BY-NC-ND 4.0 Contents 1 Introduction ..................................................................................................................................................................................... 3 2 Installation ........................................................................................................................................................................................ 3 3 Instructions for use ..................................................................................................................................................................... 3 3.1 Calibrate tab ........................................................................................................................................................................ 4 3.2 Preprocess tab .................................................................................................................................................................... 5 3.3 Optimize tab ......................................................................................................................................................................... 6 3.3.1 One pore ............................................................................................................................................................................ 8 3.3.2 Multiple pores................................................................................................................................................................ 10 3.4 Save and exit ...................................................................................................................................................................... 14 1 Introduction This document is the user manual for the correct use of the poreScanner app. The app allows a user to calculate the textile porosity and the effective porosity of surgical meshes starting from appropriately captured photographs of the mesh. The set-up and camera parameters for the photographs capturing, as well as the precautions necessary to obtain a reliable measurement, are described in Giacalone et al. “Quantifying Mesh Textile and Effective Porosities: A Straightforward Image Analysis Procedure for Morphological Analysis of Surgical Meshes” 1 . The new feature added in version 2.0 allows to predict some mechanical parameters of the surgical meshes, starting from the same photographs and with the additional indication of the weight, thickness and the strong direction of the mesh, provided by the user. The predicted parameters are the output of linear multivariate regression models built starting from mechanical data obtained in previous mechanical tests and that use a subset of the morphological output of the app as the independent variables of each model. Please, refer to Civilini et al. “A reliable and replicable test protocol for the mechanical evaluation of synthetic meshes” 2 for a complete description of the mechanical tests and the extracted parameters and to Civilini et al. “Assessing the impact of morphological parameters on the mechanical behaviour of synthetic meshes. A multivariate regression approach” 3 for details about the regression models. 2 Installation Open the poreScanner folder and double click on the .exe file to start the installation of the app: • If your Internet connection requires a proxy server, click on the Connection Settings button and then click on Next; otherwise click directly on Next. • Choose the folder in which to install the app (you can also add a shortcut in the desktop) and the click Next; • Choose the installation folder for the MATLAB Runtime and click Next; • Accept the license agreement by selecting Yes and click Next; • Click on Install and wait for the downloading process to end; • Click Finish to end the installation. You can now start the app by double clicking on the icon. 3 Instructions for use While using the app, you can access the manual by clicking on the book icons that you find in the panels. WARNING: it is recommended to use poreScanner in full screen mode. 1 DOI: https://doi.org/10.1016/j.cmpb.2023.107850. 2 DOI: https://doi.org/10.1016/j.jmbbm.2023.105987. 3 DOI: https://doi.org/10.1002/cnm.70092. 3.1 Calibrate tab After opening the app, you will be in the calibration tab (Figure 3.1). Figure 3.1 Calibration tab. Here you can calibrate the system for subsequent calculations, through two methods: • Manual calibration: Type a calibration factor if you already have one and press the ENTER key to proceed to the next step. • Automatic calibration: Click on the Load calibration image button to select a calibration image 4 and wait until the app finds the calibration column bounding circle (this will be used to calculate the calibration factor); if the detected circle (in red) correctly follows the calibration column perimeter, press the Yes, save calibration button in the dialog box to proceed to the next panel (Figure 3.2). If you want to repeat the calibration using a different calibration image, select No in the dialog box and select again the Load button. The calibration factor is computed as the ratio of the diameter of the circle in mm and the same dimension in pixels. The default value for the diameter in mm is 16.059 mm; if you need to change that dimension, use the Nominal diameter [mm] field, prompting a new dimension before clicking on the Load calibration image button. The Default button allows you to set the dimension back to the default value of 16.059 mm. 4 The calibration images are taken using a calibration column printed from a 3D model creating by the authors. The image shows the column from the above and the calibration factor is computed knowing the diameter of the white circle. For a detailed description of the set-up used and for downloading the .stl file of the calibration column, please refer to Giacalone et al (1) WARNING: the calibration factor must be expressed in mm/px. Figure 3.2 Confirm calibration dialog box. 3.2 Preprocess tab Click on the Load button to load the mesh image. A dialog box will appear, reporting the size of the picture (Figure 3.3). Before proceeding to the next panel, you must at least define a name in the Device name field: this should be the same for different images of the same device. Figure 3.3 Dialog box appearance in the Preprocess tab. The dialog box will appear after loading a mesh image. If you want to predict the mechanical parameters of the mesh, you can fill in the Weight and Thickness fields in the Predict panel to define the weight and the thickness of the device respectively, using the units of measurement displayed in the app. After that, click on the Define direction button to define the strong direction of the mesh: a dialog box will appear asking if the strong direction is already aligned horizontally; if so, click Yes, alternatively click No and define the strong direction by clicking on two points located along the strong direction in the image and pressing ENTER. After the first iteration, if you decide to analyze another image of the same device, you can use the Reload parameters button to automatically fill the Weight, Thickness and Device name fields with the same values of the previous iteration. If you want to use the entire image for the porosity computation, click on the Proceed button, otherwise define the new dimensions of the image using the Length and Height fields in the Crop panel. After that, you need to select the position of the crop rectangle on the original image. Click on the Crop button, then click a point on the image and press the ENTER key. The crop rectangle will have the top-left corner placed in the position you just clicked, while its length and height will be the ones you defined in the Length and Height fields. The image to be processed in the next steps, will be the one delimited by the crop rectangle. WARNING: if you select more than one point in the crop action before pressing the ENTER key, the app will use the first click as the position of the top-left corner of the crop rectangle. A dialog box will appear, asking you to decide if the rectangle is in the correct position. If so, press Yes, otherwise press No and select a new crop region after clicking again on the Crop button; otherwise click on the Proceed button to skip the cropping step. If the crop rectangle crosses the original image, a warning will appear, asking you to change the position of the top-left corner of the crop rectangle or the values of the Length or Height fields. 3.3 Optimize tab After clicking on the Proceed button in the Preprocess tab, the app binarizes the image and you will be sent to the Optimize tab (Figure 3.4). Here the binarized image will be shown as a yellow mask superimposed on the original image, allowing you to check if the binarization is satisfactory; if so, press the Save and continue button to save the result and elaborate another mesh image. Figure 3.4 Optimize tab. During the first iteration you will be asked to select a path for the creation of the report (see paragraph 3.4). Pressing the Save and continue button you will be sent again to the Preprocess tab; if you need to change the calibration image before processing the next image, you can click on Calibrate in the upper left part of the app to go to the Calibrate tab and change the calibration factor using the two methods presented in the Paragraph 3.1. In the Optimize tab, the binarization correction can be implemented to adjust eventual misidentified pores (highlighted by red circles in Figure 3.5). Selecting one of the options of the Choose drop-down menu, these erroneous pores can be corrected by including them in an updated binarization mask. The two options are described below. Figure 3.5 Mesh image and mask with misidentified pores. 3.3.1 One pore If you choose the One pore option, you can select the erroneous pores to fill one at a time. After selecting the erroneous pore area, press the ENTER key; a blue star will appear (Figure 3.6a and Figure 3.7a) on the centroid of the corresponding void. • If the selection is correct, selecting the Accept button a green star will appear in place of the blue one (Figure 3.6b), signaling that the pore will be filled on the first mask update. Be aware that after pressing the Accept button it will not be possible turn a green star into a red one even before pressing the Update mask button. Figure 3.6 Close up on the mesh image. a) Pore highlighted after selection; b) Accepted selection. • If the wrong void is highlighted, click on the Discard button; a red star will appear in place of the blue one (Figure 3.7b), signaling that the pore will not be filled updating the mask. Figure 3.7 Close up on the mesh image. a) Pore highlighted after selection; b) Discarded selection. NOTE: if you select more than one pore before pressing the ENTER key, only the first pore selected will be considered for filling. You can repeat one pore action as many times as you want. If in any time you want to update the mask, press the Update mask button and all the pores highlighted by a green star will be filled.