Now to start the scan.
Nope. Not yet. We have some housekeeping to do, before that happens.
The base of each specimen was flat enough that no additional materials (like wax) was needed to hold it in place. The paraffin film did a good job of keeping these relatively large (when compared to the X-Rays, of course) objects in one spot. Good. Now the specimen is in its place and its stage is mounted inside the scanning chamber. Close the door—safety first, remember? Yes, yes you do—and prepare for the beam to energize.
One of the advantages of living in today’s world is that you can make a software control your hardware without having to manually adjust things. Apparently, when they wanted to do these experiments, in the olden days, they used to manually adjust the stages for each performance (no, that was a lie). The SkyScan software was used to adjust position of the specimen—vertical, horizontal, radial, you name it.
It was necessary to adjust the voltage and current, so that the power of the X-Rays emitted but the emitter gun would always be around 10 watts and never exceeded it. This was done to adjust the contrast of the images. The voltage and current were 44 kV and 222 μA for this experiment. (Psssttt… multiply the two to get the power).
Next was an important step called Flat Field Correction, which I’m fondly going to call FFC and never use it again. This step is used to have a uniform brightness in the background and calibrate the sensor on the other side. This was when the resolution, pixel size, etc. had to be chosen.
And finally, it was time to scan. The step angle of the stage’s rotation was set to an appropriate amount to not waste the time. Smaller the angle, longer the scanning time. I’ve seen some scans happen for days!
The camera sensor was set to capture multiple images during each rotation step and average them out to reduce errors and smoothen the final image by a process called Frame Averaging. There was also Random Movement correction to take care of any dead pixels, because cameras are dainty and don’t age well.
As far as I can remember, there was also an option to turn the X-Ray off or leave it on after the scan ends—off should technically have been the only option… because we’re talking about X-Rays here.
Alright! Now, the scan has begun, and below is an image of the Scanner preparing to do its thing.
Here are some of the details I collected from the log file, because obviously, I can’t remember everything that happened in August 2017 at them moment (Yes, that was when the scan was done, and the actual project had started months before that):
Source Type = Hamamatsu 100/250
Camera = SHT 11Mp camera
Camera Pixel Size (μm) = 9.00
Source Voltage (kV) = 44
Source Current (μA) = 222
Frame Averaging = ON (6)
Random Movement = ON (8)
Vertical Object Position (mm) =33.693
Exposure (ms) = 238
Rotation Step (deg) =0.300
These are only some of the setting. There were more; I just don’t want to make these posts extremely technical. More stuff on reconstruction, visualizations, and analyses another time.