A method of operating a particle beam system, the method comprising: determining at least one deflection amount and at least one deflection time at which a first beam deflection module of the particle beam system connected to a data network of the particle beam system is to provide the at least one deflection to a charged particle beam corresponding to the deflection amount; determining an un-blank time at which a beam blanking module of the particle beam system connected to the data network is to un-blank the beam; determining a blank time at which the beam blanking module connected to the data network is to blank the beam; generating by means of a calculation module a data structure comprising plural data records, wherein each data record includes a command representing an instruction for at least one of the first beam deflection module and the beam blanking module, and a command time representing a time at which the instruction is to be sent to the data network; sorting by means of the calculation module the records of the data structure by command time; generating by means of an encoding module a set of digital commands based on the data structure, wherein one digital command is generated for each one of the records; and sending the digital commands of the set to the network in an order corresponding to an order of the sorted records; wherein at least one digital command of the set represents an instruction for the first beam deflection module to provide the deflection to the beam corresponding to the deflection amount; wherein at least one digital command of the set represents an instruction for the beam blanking module to un-blank the beam; and wherein at least one digital command of the set represents an instruction for the beam blanking module to blank the beam. determining at least one deflection amount and at least one deflection time at which a first beam deflection module of the particle beam system connected to a data network of the particle beam system is to provide the at least one deflection to a charged particle beam corresponding to the deflection amount; determining an un-blank time at which a beam blanking module of the particle beam system connected to the data network is to un-blank the beam; determining a blank time at which the beam blanking module connected to the data network is to blank the beam; generating by means of a calculation module a data structure comprising plural data records, wherein each data record includes a command representing an instruction for at least one of the first beam deflection module and the beam blanking module, and a command time representing a time at which the instruction is to be sent to the data network; sorting by means of the calculation module the records of the data structure by command time; generating by means of an encoding module a set of digital commands based on the data structure, wherein one digital command is generated for each one of the records; and sending the digital commands of the set to the network in an order corresponding to an order of the sorted records; wherein at least one digital command of the set represents an instruction for the first beam deflection module to provide the deflection to the beam corresponding to the deflection amount; wherein at least one digital command of the set represents an instruction for the beam blanking module to un-blank the beam; and wherein at least one digital command of the set represents an instruction for the beam blanking module to blank the beam.