Editing Archive (section)

=SkyScan Micro-CT Scanning=

===Settings Suggestions for SkyScan bone scanning===
''email, forwarded from Phil Salmon, phil.salmon@skyscan.be''

*Here are some guidelines for scanning bone. You will in due course be able to fine tune the scan settings for your own samples.

#<u>Get the best magnification that you can</u>, but have at least most of your object perimeter contained within the borders of your field of view. Technically it is possible to scan an internal region at high magnification with much of the object outside the field, but in practice this decreases the signal/noise ratio.  For example if you are interested primarily in trabecular bone, it is OK if some small parts of the cortical perimeter move out of the field during scanning.
#: N.B. Always <u>check your object at several angles before launching the scan</u> - e.g. 45, 90,135, 180 degree views, to check that it is rotating as symmetrically as possible).
# Voltage: What species bone are you studying? If it is anything larger than a rat I should stay with the maximum 100 kV unless you have very small samples and require maximum resolution. For mouse bones a <u>general range is 50-68 kV</u>.  Remember that you will need to make a new background or "flat field" correction when you change tube voltage or current.
# Current: Again for <b style="color:red">large bones</b> leave this at <b style="color:red">maximum</b>. However for <b style="color:red">small samples </b>you could make use of the <b style="color:red">smaller source spot </b>size option. If your machine is the 100kV 1072, then at full voltage and current (power=10W) the spot size is 8 um. 
#:However, when the <u>power falls below 4W the spot size decreases to 5um</u> (this happens automatically). If the sample <U>x-ray absorption is still OK </U>at a setting with power < 4W, you will get <b style="color:red">optimum spatial resolution</b>.
# Exposure time. Exposure time is set automatically.
#Frame averaging and step size. As you increase frame averaging and decrease rotation step, resolution will increase but so will scan time. So <U>use the maximum values that time allows.</U>
# Filter. <U>I always use 1mm Al for bone</U>, even small mouse samples. "Filter 2 and 3" actually contain no filter. So your options are 1mm Al or no filter.
# Some notes on dataset reconstruction: 
#*Set beam hardening and ring artifact reduction on the minimum settings that are visibly necessary.  
#*Set smoothing to minimum or off. 
#*Set the “cross-section to image�? upper limit just a little above the top end of the grey spectrum of the sample to optimise contrast in the reconstructed images. I usually put the lower limit halfway down the upper slope of the peak of background - some background will facilitate dataset thresholding (see next comment).
# You can use the threshold module in the program 3d-calculator to get the optimum thresholding to binary images. 
#: Download this from [http://www.eur.nl/fgg/orthopaedics/Downloads.html| here] if you don’t have it yet.

===Corrections for Ring Artifacts and Filter Use===
''email, forwarded from Alexander Sasov, sasov@skyscan.be''
# <U>If ring artifacts appear only when you scan with a filter, you should acquire new flat-field reference for that particular filter and save it. Possible reasons for the rings are switching to another voltage or current or exposure, some particles in the filter surface, cracks or just small changes in the x-ray spectrum of the source, which normally appear in several years of usage.</U>
# Normally one should acquire new flat-field references t wice per year or in the case of the appearance of strong ring artifacts. Another reason to acquire new flat-field references is a system operation with new voltage/current/exposure. Don't forget to save new flat-field references directly after acquisition.

===Specimen Holders===
''email, forwarded from SkyScan''
:<U>Scanning area for one scan in 1072-instrument can be max.20mm in diameter and 18-19mm in length.</U> Also possible to scan the big objects up to 38mm in diameter with twice scanning time. Object can move +/-10mm for positioning of scanning area or to <U>scan up to 30-35mm in length by several partial scans with automatic connection to one continuous set of cross sections.</U> 
:*Physical object length may be up to 45-50mm, but only 30-35mm can be scanned.