Is it okay to directly address your reader when writing a scientific paper? I'm currently writing a paper that has some kind of tutorial parts in it. I have written sentences similar to:

«... depending on your operating system, the procedure is different»

Is addressing the reader directly like that in a scientific paper ok? Or should I try to rewrite these sentences?
Except when outlining a motivation for a particular section in a paper, I would recommend speaking in third person as much as possible. An example of the exception is:


  Because our primary interest is in ____ we have chosen to follow the method developed by ___.


For your case I would reword your sentence as:


  Depending on the operating system used, the implementation will differ.


Always shift the focus to the things being manipulated, whether it be an experiment, computer program, or anything else.

As for your sentence in the comment you could write it as:


  How the scripts are run is at the user's discretion; it may be interactive, line by line, or in batches, depending on its function.


I have used the at the user's discretion a lot in my work; it's a professional way of saying you can do this part however you like. Also, whenever I have to identify somebody whose completing a task, I try and identify them based on the task they are completing (e.g. the analyst, the user, or the programmer). If you say you, you are assuming that the reader is the one who will be carrying out these tasks, which may not be the case.

If you have to address the reader, then you can say something like:


  For the reader's convenience, the pertinent information has been summarized in Table 5.


or the famous, albeit witty, cop out:


  _____ is left as an exercise for the reader.