USF Health


Canto II Troubleshooting

There are infinite numbers of potential technical issues with running a cytometer.  This section here is to help you with a select few. For the rest of them, well, they are part of the reason why they pay me my salary…


Start up

The cytometer is not connected to the instrument: Under “Instrument” tab pick connect.

There is not enough fluid in one of the tanks:  exchange the fluids, then hit Instrument>Cleaning modes>Prime after tank refill.  Pick the tank that is applicable and OK.  You don’t have to do this if you emptied the Waste tank.


Running the experiment

Tube is not pressurizing:  the tube is the wrong kind or the tube is cracked, transfer your sample in a good tube.  Alternatively the BAL seal at the lip of the rube might be bad, ask us to fix that.

There are no event in the plots: FSC/SSC voltages are way off. If the events either have no color or the same as background you won’t see them either, although on the acquisition panel it is counted.

Values (scatter, Fl)  are not stabile.  Bubble in the system.  Instrument>Cleaning Modes>De-gas flow cell.  If that did not do the trick, either repeat or Instrument>Cleaning Modes>Bubble filter purge and de-gas flow cell.

Data makes no sense

Think over your gating strategy; ask core staff.