It depends who your users are and what needs they have. Our users are mostly MATLAB&#x2F;Python users, pretty tech-savvy, and being able to edit individual bits of the dataset with other applications or write their own code to analyse them is an often-used feature.<p>It&#x27;s rare we ever need the whole dataset - in fact, it&#x27;s really great to be able to say to the user &quot;don&#x27;t send us your 100GB dataset: just go to the &quot;acquisition&quot; subfolder and send me the 10MB file called &quot;oscilloscope.dat&quot;&quot;. With HDF5 this is difficult enough that it&#x27;s almost always easier to send 99.9% of useless data (i.e. the whole file) when all you want is a single array within it.<p>If your users will rarely need to do this, you could just store the entire folder hierarchy in a .zip and access it using standard tools that most programming languages have. It&#x27;s worth noting that the new Microsoft Office formats do exactly this - in their case, a bunch of XML files inside a .ZIP. (Rename a .docx to .zip and you&#x27;ll see!).<p>MATLAB has moved from their own custom binary format to HDF5, which is the lesser of two evils.