How to make color-coded 3D models for structure thickness in CTVox

Transcription

1 How to make color-coded 3D models for structure thickness in CTVox Method note Page 1 of 10

2 2 Bruker microct method note: Color-coded structure thickness in CTVox Introduction When running a 3D analysis for structure thickness, one can calculate the structure thickness or separation distribution from the 3D analysis plug-in in CTAn, and plot these data in a histogram. This, however, does not provide any visual representation of how the structure thickness is distributed throughout the sample. A possible solution to this problem is to create a volume rendered 3D model in CTVox with a color code for structure thickness. This method note will illustrate step by step how to create a 3D model for structure thickness in CTVox. The sample used in this method note for demonstration is (part of) a mouse bone (femur), consisting of both (thick) cortical and (thin) trabecular bone. Part 1: Output color-coded images for structure thickness in CTAn Generating a color-coded 3D model for structure thickness (or similarly structure separation) is performed in 2 steps. First, color-coded images are created and saved for structure thickness (or separation) in CTAn, and second, these images (dataset) are loaded in CTVox to create a 3D model. As usual, the analysis starts with setting an appropriate region of interest if required (not done in this case), folowed by thresholding of the dataset using the right thresholding settings for the dataset being processed. Preview images can be found below. Raw image Binary image Page 2 of 10

3 3 Bruker microct method note: Color-coded structure thickness in CTVox In a next step, color-coded images will be created and saved for structure thickness (or separation). This function is available from the 3D analysis plug-in in the custom processing tab. Select structure thickness (or separation) for analysis (either in combination with other parameters or not) from the additional values column, as well as the option to save color-coded images of structure thickness (or separation) at the bottom of the window (see below). This method note will continue with and focus on structure thickness, although the principle is exactly the same for structure separation. As a results, a new dataset is saved, which can be opened again in CTAn. The gray scale images will all appear as uniform black images. However, changing the palette to color scale and setting the palette window sliders to color density range from the CTAn preferences menu (tools tab) will turn the images in color-coded cross-sections which are much easier to interpret. Page 3 of 10

4 4 Bruker microct method note: Color-coded structure thickness in CTVox Page 4 of 10

5 5 Bruker microct method note: Color-coded structure thickness in CTVox If wanted, the color density range can be changed (squeezed) to get an image in which different colors encode a different structure thickness. Now 2D color-coded images were created for structure thickness. The next step will go into detail on how to create a color-coded 3D model for structure thickness. Page 5 of 10

6 6 Bruker microct method note: Color-coded structure thickness in CTVox Part 2: Create a color-coded 3D model for structure thickness in CTVox Color-coded 3D models for structure thickness are created in the CTVox volume rendering software. The histogram of the dataset (shown in the left corner of the program window) now doesn t correspond anymore to the grey scale histogram of the dataset, but to structure thickness. Each class number from the structure thickness distribution histogram is thus represented by a grey value. Setting a transfer function thus comes down to assign a color gradient according to structure thickness. In this case, thin structures are represented in red, which changes to green and finally blue when structure thickness increases. It was not very easy to make a transfer function for thickness maps in early versions of CTVox as the histogram is very narrow due to the small number of grey scales (corresponding to the thickness intervals). However CTVox version 2.7 onwards allows stretching of the horizontal axis of the transfer function graph, allowing detailed TF structure at very low densties as shown below: Page 6 of 10

7 7 Bruker microct method note: Color-coded structure thickness in CTVox Note: An alternative solution to focusing the transfer function gradiants at very low grey scale values is to expand this histogram and make it easier to set the transfer function. This can be done in CTAn version onwards in custom processing, using arithmetic functions which the histogram. In this case, the arithmetic function MUL (multiply) was applied to multiply the values of the histogram with a factor 20. This expands the histogram over the full range of available grey values (0-255) as can be appreciated from the table below. Page 7 of 10

8 X 20 Original 8 Bruker microct method note: Color-coded structure thickness in CTVox Image Histogram Following the arithmetical operation, don t forget to save this new dataset by running the save bitmaps plug-in from the custom processing tab. Page 8 of 10

9 9 Bruker microct method note: Color-coded structure thickness in CTVox The new dataset can now be opened again in CTVox to create the color-coded 3D model for structure thickness. As illustrated below, the expanded histogram makes it easier to adequately set the transfer function. Again, thin structures are represented in blue, which changes to green, red and finally white when structure thickness increases. Page 9 of 10

10 10 Bruker microct method note: Color-coded structure thickness in CTVox Additional illustration: blood vessel network (perfused with BaSO 4 ) of part of the rat lung (80 µm pixel size). Thin structures are represented in red, which changes to green and blue when the vessel diameter increases. Page 10 of 10