Method note. Page 1 of 7

Transcription

1 Advanced image coregistration in Dataviewer Method note Page 1 of 7

2 2 Bruker microct method note: Advanced image co-registration Introduction The 2D and 3D image co-registration in Dataviewer provides a powerful tool to coregister datasets and save them in the same orientation. A different method note (MN044_Image and dataset registration in Dataviewer) illustrates how to run a basic image or dataset co-registration in Dataviewer. However, for some datasets with big internal changes in morphology, this basic co-registration may not be suitable. In such cases, it would be easier to do the matching or co-registration on the global shape of the object, ignoring the internal structure. An example of such case can be co-registration of bones. The overall shape of a specific bone (e.g. a tibia or femur) is very well conserved, while the internal morphology (the trabecular structures) is highly variable upon age, treatment, etc. This method note illustrates how to do this in practice, using SkyScan CTAn and Dataviewer software. Step 1: Save binary dataset without internal structures The datasets used for this method note represent a mouse tibia of an ovariectomised (treatment) and sham-operated (control) mouse. Due to this treatment, the internal trabecular morphology of the bone significantly changes (bone loss upon treatment). Co-registration of these datasets is required when one wants to investigate for example where bone loss occurs, or wants to make identical movie animations for both datasets. The big changes in internal morphology, however, impede the automatic match all co-registration option in Dataviewer. A better approach is to run the co-registration on the overall shape of the bone, excluding the internal structures as landmarks for the image co-registration. To do so, we will save a new dataset representing a binary selection of the outline of the bone. The most straightforward way to do this is by running the following task list in the CTAn custom processing page: 1. Threshold the dataset adequately 2. Run a 2D shrink-wrap operation 3. Save the resulting region of interest as a new binary dataset Page 2 of 7

3 3 Bruker microct method note: Advanced image co-registration This task list can be extended by a despeckling or closing operation after step 2 when needed. The final outcome should be a white selection of the object without any pores left inside (Figure 1). Figure 1. Save binary dataset without internal structures in CTAn software. Step 2: Co-register binary datasets The new binary datasets can be found in a new folder inside the folder containing the original data. Both datasets, representing the global structure of the object, can now be loaded in the 3D registration window of Dataviewer (Figure 2) and registered to each other (see MN044_ Image and dataset registration in Dataviewer for more information). One can either manually match the datasets, or in this case also select the register all option to match the two datasets automatically (Figure 3). At this point, one can save three different datasets: the reference dataset, the target dataset registered to the reference dataset and the difference dataset. However, these data correspond to the binary datasets and thus not to the original greyscale data. Page 3 of 7

4 4 Bruker microct method note: Advanced image co-registration Figure 2. Binary datasets loaded in 3D registration window before matching. Figure 3. Binary datasets loaded in 3D registration window after matching. Page 4 of 7

5 5 Bruker microct method note: Advanced image co-registration Instead of saving new datasets, we will copy the transformation applied to the binary data to the original greyscale data now. On the right side of the 3D registration window, one has the option to save the transformation parameters in a log file by clicking the keep button (Figure 4). Note that the transformation is only applied to the target dataset. One will thus only be able to find these transformation parameters in the log file of the (binary) target dataset. Figure 4. Upper: clicking the keep -button will save the transformation parameters in a log file that can be found in the folder containing the binary data of the target dataset. Lower: Screenshot of the log file containing the transformation parameters of the binary target dataset Page 5 of 7

6 6 Bruker microct method note: Advanced image co-registration Step 3: Copy the transformation parameters of the binary dataset to the original dataset To apply the same transformation of the binary target dataset to the original greyscale (target) dataset, one has to select the entire [Coregistration] parameter section (see Figure 4 lower panel), and copy this to the bottom of the log file of the original greyscale target dataset (Figure 5). Figure 5. Copy the transformation parameters from the binary target dataset log file into the log file corresponding to the original grey scale target dataset. Step 4: Save a copy of the transformed target dataset Copying the transformation parameters to the log file of the target dataset does not immediately affect the dataset orientation upon opening in Dataviewer, CTAn, software. To apply the transformation settings, one still has to save the target dataset in its new orientation. To do so, load the original grey scale datasets in the 3D registration window of Dataviewer. Make sure not to switch the target and reference dataset compared to the binary datasets. At this point the transformation data copied in the log file of the target dataset are applied to the target data (Figure 6). If necessary, one can still further fine tune the registration Page 6 of 7

7 7 Bruker microct method note: Advanced image co-registration parameters. The only thing left now is to still save a copy of the transformed target dataset by clicking Save and selecting the desired file format. Figure 6. Original grey scale data loaded in 3D registration window. Registration was done by copying the transformation parameters in the log file of the target grey scale dataset. Page 7 of 7