How to make and open surface rendered 3D models

Transcription

1 How to make and open surface rendered 3D models Method note Page 1 of 13

2 2 Bruker-MicroCT method note: Surface rendered 3D models Introduction The goal of this method note is to illustrate step by step the process of how to set up a basic custom processing protocol to make (and open) surface rendered 3D models. More advanced protocols can be found in other method notes, for example on how to make different models for the open and closed porosity of a sample or color coded 3D models of pore or particle size. As an illustration, a hydroxyapatite (HA) scaffold is used. Looking at the reconstructed images, one can see that the scaffold has a porous structure (the pores being air bubbles), but also contains some high dense particles (see image below). Unlike volume rendering, where a dataset of 2D greyscale images is loaded into the volume rendering software (CTVox), surface rendering is based on thresholding of a structure or density of interest followed by the generation of a 3D model of these selected parts. Page 2 of 13

3 3 Bruker-MicroCT method note: Surface rendered 3D models Part 1: Regions of interest page Often surface rendered 3D models can be rather large and thus difficult to open or work with as the computer may run out of memory. Therefore, it is important to select regions of interest or even resize data upon loading. By clicking the Open dataset button in CTAn, browse to the reconstructed images of the sample to be analyzed. When the dataset dimensions are too large to be processed by the computer, the dataset can be resized by ticking the resize by box and specifying an appropriate resizing factor. When required, one can first select a region of interest for the dataset. To do so, browse to the Regions of interest page upon opening of the dataset in CTAn. Depending on the sample or application, one has the choice between either several geometrical shapes or a freehand selection as region of interest. By clicking the ROI dimensions, one has the possibility to predefine exactly the dimensions of the ROI if wanted. In this case, a circular region of interest with a diameter of 500 pixels was selected completely within the HA scaffold structure. Page 3 of 13

4 4 Bruker-MicroCT method note: Surface rendered 3D models In a next step, also the top and bottom of the region of interest (in the Z-direction) have to be specified. To do so, right click the slices to be determined as the top and bottom of the region of interest and select Set top of selection or Set bottom of selection, respectively. Finally, this region of interest can also be saved by clicking the save ROI button. This option is required to process multiple datasets in batch as will be explained later on in this application note. Of note, reopening the new VOI dataset greatly reduces the data volume to process, and will thus greatly speed up the analysis and generation of the 3D models. Do not forget to reload the region of interest as well (automatically saved by CTAn) from the dataset folder to delineate the dataset. Page 4 of 13

5 5 Bruker-MicroCT method note: Surface rendered 3D models Part 2: Binary images page Once an appropriate region of interest (in 3D called volume of interest) is selected, proceed to the Binary images page. In the Binary images page, a threshold has to be set to select certain structures based on the grey values. Setting the appropriate threshold can be done either by shifting between and comparing the raw image (press ALT+1) and the binary image (press ALT+3), or by setting the threshold using the Toggle halftone view function. In this case, the HA scaffold structure is selected by putting a threshold from 60 to 255. The high density particles inside the HA scaffold are selected by putting the threshold from 150 to 255. Low dense matrix selection High dense particle selection Note that when comparing different samples, the threshold values have to be kept constant for all samples. Therefore, one has to verify that the selected threshold values can be applied for all samples, which is only possible when all samples are scanned and reconstructed with the same settings. After selecting the structure (density) of interest, a surface rendered 3D model can be created by clicking the create 3D-model button according to the 3D surface construction algorithm selected in the file-preferences-advanced menu. Three algorithms can be used to create the 3D model: Page 5 of 13

6 6 Bruker-MicroCT method note: Surface rendered 3D models Marching Cubes: a surface building algorithm based on an explicit hexahedral voxel model. Double Time Cubes: a Marching Cubes type method but with approximately half the number of facet triangles, with more smoothed surface detail. Adaptive Rendering: a sub-voxel smooth rendering method allowing specification of locality and tolerance variable parameters. Locality defines the distance in pixels to the neighboring point used for finding the object border. Increasing this value allows jumping through noise on the object border, but small objects (often created by binarization of noise) with size less than this parameter will be lost. Tolerance defines the sub pixel accuracy with which the object border is delineated. Reducing this number makes the model more smooth and accurate, but increases the model file size. Additionally, upon saving the 3D model, one can choose between 4 different file formats: STL: Stereolithography, an industry standard surface rendered model for inputting into other software. P3G: A flexible format allowing smoothing of the surface in the CT-volume viewing software. CTM: A general purpose model format with good stability at very large model sizes. PLY: A computer file format known as the Polygon File Format or the Stanford Triangle Format. In practice, one will make surface rendered 3D models only very rarely in the binary image page as no image processing, for example despeckling functions to remove noise, is possible in the binary page. One will rather use the custom processing page, which contains several image processing tools, to make surface rendered 3D models. Page 6 of 13

7 7 Bruker-MicroCT method note: Surface rendered 3D models Part 3: Custom processing page Once the appropriate threshold values are selected, proceed to the Custom processing page. A copy of the dataset will be loaded. Three important buttons are on the right side of the plug-ins bar: image view image inside ROI view ROI view As you have just loaded a copy of the dataset into the custom processing page, the initial settings are: Image view Image inside ROI view ROI view In order to select the HA matrix, run the thresholding plug-in (global) using the selected values ( in this case). Note that when you select the default option, CTAn will upload the values that you have selected last in the binary page. Page 7 of 13

8 8 Bruker-MicroCT method note: Surface rendered 3D models Image view Image inside ROI view ROI view Due to noise, certain pixels can be segmented and appear as white dots or speckles. Therefore, the next step is to run a despeckling function, removing white speckles in 3D that are smaller than for example 10 voxels in this case. Note that this preset has to be optimized according to every individual application, based on the size of the white speckles. Page 8 of 13

9 9 Bruker-MicroCT method note: Surface rendered 3D models The final step is now to make a surface rendered 3D model of the scaffold matrix by running the 3D model plug-in. One can see that the different construction algorithms and file types can also be specified here, regardless of what is selected in the filepreferences menu. In this case the double-time cubes algorithm was used and a 3D model was saved from the image inside ROI as.ctm file. In the second part, the high dense particles will be selected to make a second 3D model. However, this requires reloading of the image. Image view Image inside ROI view ROI view Run the thresholding plug-in (global) using the selected values for the high dense particles ( in this case). Page 9 of 13

10 10 Bruker-MicroCT method note: Surface rendered 3D models Image view Image inside ROI view ROI view Again, one can choose to apply a despeckling function, removing white speckles in 3D smaller than for example 10 voxels. Page 10 of 13

11 11 Bruker-MicroCT method note: Surface rendered 3D models Image view Image inside ROI view ROI view Again, the last step is to make a surface rendered 3D model of the high dense particles by running the 3D model plug-in. Again, the double-time cubes algorithm was used and a 3D model was saved from the image inside ROI as.ctm file. Page 11 of 13

12 12 Bruker-MicroCT method note: Surface rendered 3D models As mentioned before, one can make 3D models for multiple samples in batch mode. To do so, select the Batch manager icon in the custom processing tab. The different steps (thresholding, despeckle, bitwise operations,.) can be saved in a task list. Therefore each plug-in needs to be added to the task list by clicking the + button (custom processing tab) or add button (top level Batch manager). You can apply the task list to several datasets using the batch manager (bottom level). In the batch-manager window, one has to add the datasets you want to analyze, as well as load the ROI for each dataset. Both the analysis protocol and the sample list can be exported if wanted. Page 12 of 13

13 13 Bruker-MicroCT method note: Surface rendered 3D models Part 4: Open surface rendered 3D models in CTVol Surface rendered 3D models can be opened in SkyScan CTVol software by clicking the open 3D model button. Note that one has to set the file type to the right format corresponding to the file format of the models that have been created, in this case.ctm. In analogy with the volume rendering software CTVox, CTVol allows 3D visualisations, but not (3D) calculations. As output, both software programs only allow to save screenshots and movie animations of the 3D models. In contrast to CTVox, multiple 3D models can be loaded into CTVol one after the other. As such, one can change the position, orientation, color, transparency, etc. of each individual model relative to the others. However, the goal of this method note is not to give an overview of all possibilities of CTVol as all those are listed in detail in the CTVol manual, but only a flavor of what is possible. In this case, the scaffold matrix was turned into grey and set transparent, while the high dense particles are represented in orange. As such, one can get an impression of how the high dense particles are distributed along the scaffold matrix and use it to visually confirm the calculations made in CTAn. Page 13 of 13