In Bioinformatics, typically analysis looks like a tree, where if you trace the analysis back it all originates from one original raw data file that came from the actual wet lab experiment. In iMaps these initial raw data files, along with their associated metadata, are used to initialise Samples.
Samples can be thought of as a way of keeping all the data from a single sequencing experiment together, and easily traced back to its source. Any Data generated from Sample data will itself belong to that Sample, so you can easily see at a glance the data belonging to a given experiment.
iMaps Samples contain metadata describing the scientist who performed the experiment, some experimental conditions, and quality checks of the original file.