NRecon Standard Operating Procedures

Created on:

January 4, 2008

1. Open NReconServer.exe by double clicking on its icon on the desktop2. Open NRecon.exe by double clicking on its icon on the desktop3. Select a file from the scanned dataset you wish to reconstruct (NRecon.exe will realize the file

was a part of a complete dataset) and click �“Open�” (figure 1)

Figure 1: Open a dataset by selecting a single file within its folder

4. NRecon.exe will allow you to begin working in the parameters tab; as a default, set thesmoothing value to Zero, the Ring Artifact Reduction to 6, and the Beam Hardening Correctionto 40%; do not alter the preset post alignment value at this time (figure 2)

Figure 2: Set the Smoothing, Ring Artifact, and Beam Hardening parameters to their default values

5. Select the tab marked �“Reconstruction�”6. Zoom In/Out until the entire scanned sample can be seen7. Adjust the upper and lower vertical lines to define the thresholding limits (figure 3)

Figure 3: Select the appropriate upper and lower thresholding limits

8. Single click the button that reads �“Prj 0000�” and rotate the sample within the window using thehorizontal sliding bar; note whether the sample remains within the field of view for all rotationsand select �“Close�” (figure 4)

Figure 4: Click on the �“Prj 0000�” button and rotate the sample image

9. Return to the �“Parameters�” tab; place a check mark in the box that corresponds to the �“objectsize > field of view�” box if the sample was outside the box at any rotation step (figure 5)

Figure 5: Location of the �“Object size > field of view�” box

10. Return to the �“Reconstruction�” tab; make sure the values within the �“Position�” and �“Fastest�”boxes are identical ; single click the �“Preview�” button (figure 6)

Figure 6: Reveals the location of the Position, Fastest, and Preview buttons

11. Set the thresholding value by dragging the green, vertical bar corresponding to the upperthresholding limit to the left or right; the �“Inverse�” box can also be checked if you wish the airsurrounding your scanned sample to appear white within the reconstructed cross sections(figure 7)

Figure 7: Adjust the Upper and Lower Thresholding Limits using the vertical bars

12. Return to the �“Reconstruction�” tab; single click the �“Fine Tuning�” button; choose the selectionassociated with �“Ring Artifact Reduction;�” Input 5 and 3 for the �“Number of Trials�” and�“Parameter Step,�” respectively; Select �“Start�”; Single click the �“OK�” button (figure 8)

Figure 8: Process used to generate the Ring Artifact fine tuning images

13. Five images will be generated (figure 9); Use the Up/Down Arrows to select the value thatrepresents the image with the least amount of visible rings; single click the �“Parameters�” tab

Figure 9: Ring Artifact Reduction fine tuning images

14. Return to the �“Reconstruction�” tab; single click on the �“Fine Tuning�” button; select the �“BeamHardening Correction�” box, 5 trials, and a �“Parameter Step of 20; Hit �“Start�” then �“OK;�” Selectthe beam hardening corresponding to the image with the most uniform grayscale (figure 10);Return to the �“Parameters�” tab

Figure 10: Beam Hardening Correction fine tuning images

15. Return to the �“Reconstruction�” tab; single click on the �“Fine Tuning�” button; select the �“PostAlignment�” box, 5 trials, and a �“Parameter Step of 1; Hit �“Start�” then �“OK;�” Select the postalignment corresponding to the image that is most well defined (crisp dots, connected circles,and no tails on the sample�’s surface), as seen in figure 11; Return to the �“Parameters�” tab

Figure 11: Post Alignment fine tuning images

16. Return to the �“Reconstruction�” tab; Select the �“Start�” button if you want to reconstruct a singledataset or select �“Add to Batch�” to add the dataset to the reconstruction queue

Created by:

David HeldtApplications EngineerTel: 610 366 7103Fax: 610 366 7105E mail: david.heldt@microphotonics.com