Apogee Flow Cytometer Help Centre

The cell data looks abnormal but the instrument settings are thought to be correct.

Why  Dirty tubes or flow cell.

To do  Run calibration beads to verify instrument performance.

Run a sample of water or buffer to verify the fluid tubes are clean. A 'Flow Cell Clean' operation should help (service tab of histogram software).

Why  Reagent problems.

Try an alternative reagent source/batch.

The histogram software on an external PC doesn't communicate with the PC Control software running on the flow cytometer's computer.

Why  No LAN connection due to:

  • Software crash or multiple copies of software running
  • Hardware fault
  • TCP/IP LAN configuration error

To do  Reboot the machine and the PC. Check the network cable connection on the rear panel of the cytometer and PC.

Repeat the instrument start up procedure (above).

Check that the 'Connect to FCM' check box is checked in the User Configuration program and click 'Save and Run FCM Software' to test again.

Make sure all network connections have been established before the PC Control program runs. Changing the network connections while the PC Control program is running may cause communication problems.

The sample does not automatically run when the sample arm is moved to the run position.

Why  Software timing error.

To do  Move arm down and up again, or click the 'Run' button in the histogram software.

Why  Autosampler status error.

To do  If an Autosampler is installed, make sure the cover is closed and the Autosampler 'Z' sensor is engaged (see Autosampler chapter).

The sample arm is not fully in the run position (the magnetic sensor needs to be engaged by the magnet in the sample arm body.

The flush doesn't start automatically

Why  Software timing error.

To do  Move arm down and up again, or click the 'Run' button in the histogram software.

Why  Autosampler status error.

To do  If an Autosampler is installed, make sure the cover is closed and the Autosampler 'Z' sensor is engaged (see Autosampler chapter of operator manual).

The sample arm is not fully in the run position (the magnetic sensor needs to be engaged by the magnet in the sample arm body.

The acquisition rate (events/second) is erratic

Why  There may be an air bubble inside the sample syringe or the sample syringe may be worn.

To do  Remove the air bubble by clicking on the “Remove air in syringe” button on the Service tab of the Control Panel. Then test the counting accuracy and stability with calibration beads to verify the condition of the syringe (operator manual section 11.2)

The PMT noise level is high (it should be less than 1.00 for all detectors)

Why  The flow cell is dirty or the PMT voltage is too high.

To do  Run several flow cell clean routines using the button on the Service tab of the Histogram software.

Use a higher software gain and reduce the PMT voltage.

Why  The OL&FC assembly (flow cell) is damaged

To do  Contact Apogee for technical assistance. (support@apogeeflow.com)

Incorrect calibration bead histogram channel number: the calibration beads fail to appear in the correct histogram channel (+/-25%) with your standard settings (PMT Voltages, Software Gain Settings, Subtraction settings)

Why  Optical fault

To do  Check the background levels (see above) and if necessary perform a flow cell clean procedure.

If the background levels remain high, use more software gain and lower PMT voltages.

Why  Fluidics fault

To do  Check the connections to the fluid box.

Perform a 'New Sheath' and 'Flow Cell Clean' procedure (service tab of histogram software) to remove air from the sheath fluid system and clean the tubes.

Perform the 'Remove Air in Syringe' procedure from the Service tab of the control panel.

The absolute counting accuracy of the machine is poor.

Why  The test beads have deteriorated (e.g. clumped into more doublets, triplets etc.)

To do  Check the test beads have been stored correctly and have not expired.

Why  Air may have collected in the sample syringe.

To do  Click the 'Remove Air in Syringe' button on the Service tab of the Control Panel. This automatically removes air from the sample syringe.

Why  The syringe is damaged or worn.

To do  Instruct a technician to replace the syringe (refer to Operator Manual, section 11.2 for guidance).

Bad CV on calibration sample

Why  Sample stream misaligned in the flow cell.

Remember that high sample flow rates give high CVs.

To do  Check that you have selected the normal sample flow rate.

Perform a 'Flow Cell Clean (Service Tab of Histogram Software) to release any air bubbles which may be perturbing the sample stream.

Bad CV on calibration sample

Why  Low sheath flow rate gives high CVs.

To do  Check the sheath pressure (sheath fluid flow rate) is set normally. Try increasing it.

Perform a 'Flow Cell Clean (Service Tab of Histogram Software) to release any air bubbles which may be perturbing the sample stream.

Bad CV on calibration sample

Why  Beads sample deteriorated.

To do  Try different calibration/test beads.

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