# Incorporating Clinical Imaging into the Delivery of Microbeam Radiation Therapy
## 3 Results and Discussion
### End to End Plantom Test  
An upper limit to the image-guided alignment accuracy can be established by evaluating the constitute errors as outlined in Table 1 below. The accuracy of the DynMRT stage calibration is limited to within a pixel deviation on the imaging detector. [PERSON]'s pixel size of \(0.006\,\mathrm{mm}\) will be taken as the limit of accuracy here. The Siemens SOMATOM go.Up produced reconstructed images with \(0.3\,\mathrm{mm}\times 0.3\,\mathrm{mm}\times 0.3\,\mathrm{mm}\) resolution. This is the limiting accuracy for identifying the tumour location as well as the location of skeletal landmarks. The accuracy of the planar radiograph used to image patients on the DynMRT stage is limited by the effective spatial resolution of the Hamamatsu flat panel detector with \(0.16\,\mathrm{mm}\times 0.16\,\mathrm{mm}\) per pixel. The stage motors display some mechanical slack when changing translation direction, precise to within \(0.001\,\mathrm{mm}\). The combined uncertainty of targeting accuracy, \(\pm 0.34\,\mathrm{mm}\) may be considered as a treatment planning margin. A suitable treatment field should encompass the intended target including this treatment margin. From the CT images obtained, an alignment phantom was created and 3D printed in polylactic acid (a thermoplastic polyester) on a fused deposition modeling printer. The phantom was an anatomically simplified model of a rat skull containing a hole centred \begin{table}
\begin{tabular}{c c} \hline DynMRT Stage Calibration & \(\pm 0.006\,\mathrm{mm}\) \\ CT Image Resolution & \(\pm 0.300\,\mathrm{mm}\) \\ Planar X-ray Image Resolution & \(\pm 0.160\,\mathrm{mm}\) \\ Stage Motor Accuracy & \(\pm 0.001\,\mathrm{mm}\) \\ Combined Uncertainty of Accuracy & \(\pm 0.340\,\mathrm{mm}\) \\ \hline \end{tabular}
\end{table} 
Table 1: Sources of positional accuracy contributing to the limiting accuracy of the alignment protocol. Figure 5: The iodine loaded phantom imaged at 80 kVp in the Siemens SOMATOM go.Up CT scanner, reconstructed using all available reconstruction kernels. Ranked from highest performing (**left**) to lowest performing (**right**). on the previously identified tumour location. A 3.2 mm diameter steel ball bearing was inserted into the hole, as shown in Figure 6. This phantom provided a rigid body with relevant anatomical landmarks and a well-defined target (in the location of the tumour) easily identifiable in CT and radiographic film images. As such, this phantom served as a tool for end-to-end verification, testing if accuracy was sufficient to proceed with in vivo studies. The phantom was placed in the same stereotactic surgical frame to be used for in vivo studies, then scanned in the horizontal position using the Siemens SOMATOM go.Up CT scanner with 0.6 mm slice thickness and reconstructed 300 um \(\times\) 300 um \(\times\) 300 um voxel resolution. The scan was reconstructed to produce a stack of coronal images then imported into Fiji [37] and rotated about all three axes to align the scan with the intended treatment frame. To replicate the handling process that may be applied to animal studies, the rat phantom was removed from the stereotactic frame and transported to Hutch 2B where it was again mounted with the stereotactic frame that was, in turn, mounted vertically to the DynMRT Stage. The stage was rotated to face the orthovoltage X-ray tube and imaged as outlined above. The two images displayed in Figure 7 were then co-registered using SyncMRT as described above, using only the six pre-defined skeletal landmarks. The location of the ball bearing was then inferred within the DynMRT stage co-ordinate system, aligned to the treatment field and treated in the AP position. Figure 6: The three top images are CT reconstructed volumes of tumour a bearing rat skull, highlighting the brain volume (red) and tumour volume (green) for a range of angles from LR to AP.