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Long Term Instrument Storage

If you need to shut down your Aurora or Northern lights cytometer for an extended period of time (e.g. more than 1 week), follow the steps below to properly clean and decontaminate the fluidic lines to ensure the system will operate smoothly when it is time to turn it back on.


  • Approximately 1L of 10% bleach (10% is diluted Clorox household bleach, which is around 6.0% sodium hypochlorite)
  • Approximately 2L of DI water - this is key to prevent bacterial growth in the lines while the system is off
  • Two 5mL polystyrene tubes containing 3mL 10% bleach
  • Four 5mL polystyrene tubes containing 3mL DI water


  • While the instrument is on and connected to SpectroFlo, go to the Cytometer Menu.
  • If time permits, perform an overnight Contrad soak to thoroughly clean the flow cell by running Fluidics Shutdown with 2 modifications:
    • In Step 4, load another tube containing 3mL 25-50% Contrad.
    • Once Fluidics Shutdown is completed, remove the Contrad tube from the cytometer and load a tube containing approximately 1mL DI water.
    • Power off the system and leave it overnight.
    • The next morning, power on the instrument and connect to SpectroFlo.
  • Run a Long Clean following the steps in the wizard. If you are using a saline-based sheath fluid, use diH2O at step 4 (minute 4.12) of the Long Clean. Long Clean Video Tutorial
  • When the Long Clean has completed, run Fluidics Shutdown. Instead of running the tubes prompted by the software wizard (10% bleach, DI, 30% contrad, DI), ONLY run DI water tubes.
  • When the Fluidics Shutdown is complete, power off the instrument and leave a tube containing approximately 1mL DI water on the sample injection port (SIP).  This will keep the sample line wetted and prevent it from drying out.

Resuming Operation

  • When you are ready to use the instrument again, power on the instrument.  
  • Open SpectroFlo, log in, and wait for the software to connect.
  • Optional: If you'd like to replace the DI water in the system with a different sheath, run a Long Clean using 10% bleach, and then your desired sheath.
  • Open a Default Experiment and set flow rate to Medium.
  • Load a tube containing approximately 2mL DI water and click start.
  • After 30 minutes, click Stop.
  • Run QC to ensure the cytometer is functioning properly.