The guidelines sketched here are a walkthrough on how we organize our tomographic data sets in the BioEM lab of the University of Basel.
We use a series of conventions for the storage of the raw data (i.e.) tilt series, in order to make easy to keep track on the processing steps already performed (alignment, reconstruction), the location of the intermediate results, and their binding into a Dynamo catalogue. The idea is to keep and uniform naming convention that allows to comfortably locate the sought files and folders with simple Linux commands.
In this example, we assume that you are using imod for tomographic alignment and reconstruction of each tilt series. The raw data is stored in a tree below a repository folder, which will contain all the data (tilt series and tomograms) related to the tomography projects. The repository folder is created with the structure:
<repository>/data <repository>/ctf
Here, <repository> is some location in your file system, probably a file share destined for massive storage (at least Tbs). We often call this location 'repository' (literally).