Saving

After Calibration, you'll need to properly save your file so that it follows naming protocol.

Double check that your parameters are correct and that you have entered filter information into the Filter dialogue on the toolbar if necessary, then click New. You can save your scan into one of two linked directories on the reconstruction computer. Check that there is enough space in the directory you are using.

To archive data in a meaningful way, here is a description of naming protocol. Use underscores (_) in place of spaces and avoid unusual characters in names (such as \ / * etc).

You should use two levels of directories to archive scans. The top level is called the Parent Project folder. If you are doing multiple scans for a study about shells, use a name that starts with a descriptor of the project (shells), then who this project is for (use your or your PI's name), then the year, all separated by an underscore. In this example, the Parent Project folder may be called Shells_Smith_2015.

The directories under the Parent Project folder are used for individual scans and is called the Scan Sample folder. Each scan must have its own Scan Sample folder. The name used for the Scan Sample folder should be descriptive of the scan, using a species name or specimen number where appropriate and you may want to end the name with an iterative number (like 01) in case you decide to rescan. Following the above example, I may name a scan specimen#_01. On the other hand, if I am scanning multiple bones from the same animal, I may choose to name my Scan Sample folder didlephis_forelimb.

Within each Scan Sample folder you need to create a raw data folder, which should be named RawData. This is where the scan is saved along with all metadata files. Tiff or DICOM stacks generated from this data should be saved in a separate image stack folder (named ImgStack, Tiff_stack, etc). There should also be a ScanSheet.pdf generated from the database, which contains information about the specimen and scanning parameters.