TROUBLESHOOTING FLOW CHART

Have a cold
beverage.
Revised and updated on January 16, 2003, by FACScan(FC)\FACSort(FST)
Tony Leger and Automation Lab Technology. FACScalibur (FCB)
Fluidics/Pneumatics DCM is the acronym for YES
troubleshooting guide droplet containment module.
SIP is the acronym for sample
injection probe

NO Is the
Is there a No Is Sample Is leak YES No YES YES instrument
puddle of injection coming from Are there Is there a Is the
passing the
fluid under probe sheath or any fluid sample flow rate
daily QC
the dripping? waste tank leaks? flow rate? stable?
protocol
Cytometer ? area?

No No
YES
YES SIP may be
YES clogged See
YES See trouble Is Instrument
shooting status NOT
Section 6 NO
See trouble
Open fluidic No shooting
section 4 for READY? step1 for help
Is DCM pump help
door (FC/FST) running when section 1
and remove right the sample
side panel. See
arm is to the YES troubleshoot
(FC/FST/FCB) side?
NO ing
Section
Problem
YES 7 for help
solved?
See
See trouble Yes troubleshooting
Is instrument
shooting aids staying in
section 1 for Section 5 for STANDBY No
Assistance Remove right side help
Check in all cover and See
locations shown troubleshooting Replace the
in section 1 for three
section 2 for help hydrophobic
leaks. No filters. See
figs.3.2 and
Proceed to 5.1 for
troubleshooting
locations
section 6 for help
It sounds like
you have a clog
in you waste line.
Remove right YES
side cover and
Problem
See trouble
solved?
shooting section
3 for help.

No
Call for further
The pictures in the proceeding troubleshooting section are of assistance
the FACScan. The sub-assemblies of the FACSort and
FACScalibur are functionally similar, however, some are
located in different locations.
Troubleshooting Section 1
Figures 1.1-1.4 show where leaks may be possibly coming from. Before disconnecting fittings make sure to de-pressurize the
sheath tank. Follow all general Lab safety precautions when working on instrument.

Fig. 1.1 Sheath/Waste Fluid Area Fig 1.2 Flow Cell Area**
Check around sheath Check male and female, Remove waste tank Check to see if waste
tank neck, and level white and orange quick and check for leaks. (black line) barb fitting Check sides of
sensor cap for air leaks disconnect fittings. Check Check around the is broken. viewing orifice for
(hissing sound). fittings to the right of waste seam area of the drips. If drips are
tank (dashed line). tank. present suspect
black line barb
fitting leaking or o-
rings on top and
bottom of viewing
orifice to be
defective.

Check to see if Sheath

input (clear line) barb
fitting is leaking.

The green line is

the sample pressure
line. If it is leaking
Remove sheath tank and Check top and bottom of Check to see if
here system will
check for tank leaks. Most saline filter for leaks. drain (blue line)
stay in STBY and
leaks occur around the neck Also check quick barb fitting is
sample tube will
or along the seam. disconnect fittings. leaking.
fill.

Fig 1.3 Fluidics Box Fig 1.4 Bulkhead Fittings

Also check white
Check orange waste fitting for leaking and
bulkhead fitting for for the trail of
leaks. Check for dripping saline.
trail of dripping
saline below
fittings.

*Pictures are sub-

Check white barb assemblies of the
fittings for leaks
FACScan .

** Follow
manufactures safety
precautions when
Check for viewing flow cell with
pooling optics cover removed
leaks here.
Check clear tubing For viewing ease, the sample injection probe (SIP) has been removed.
in pinch valves. When checking this area for leaks using a flashlight and inspection mirror
Both sides. will be of assistance.
Home
 Troubleshooting Section 2
Fig 2.1 SIP (bottom view) Fig. 2.2 DCM pump
Differential pressure regulator DCM is the acronym for droplet
Step 3. Loosen one containment module.
Step 1. Remove C-clamp side of clamp with SIP is the acronym for sample
DCM tubing from thumb screw or injection probe
barb fitting and pull using hex key.
it gently enough to
Air
get syringe on the
pump
end.

Droplet moves
up the outer Droplet
sleeve of the SIP from
to the barb fitting pump to
waste Tubing
on the rear of clamp
flow cell.

Step 2. Remove black

DCM tubing from this
Droplet point.
from SIP to
the pump

In order to troubleshoot in this section you will need a syringe, DI water, 10% Fig. 2.3 Sheath/Waste Fluid Area
bleach, and a 3/32” hex key.

Look here for fluid to flow through the orange

Steps for flushing the Droplet Containment waste fitting
Module (DCM) lines.
1. De-pressurize sheath tank and place Instrument in STBY.
2. Remove DCM tubing from the rear of the flow cell (step 1).
3. Separate DCM tubing at barb fitting between Sample Injection
Probe (SIP) and DCM pump (step 2.).
4. With syringe and 10% bleach flush tubing between SIP and
DCM pump. If fluid flows easly, then chances are the clog is in
another line, proceed to step 4. If the line is clogged press hard
on syringe and look for fluid flow. If clog is too stubborn call
Tritech for replacement tubing.
5. Lossen the DCM pump clamp (step 3).
6. Flush 10% bleach through DCM pump tubing and the waste line.
Monitor the waste as shown in figure 2.3, for the flow of fluid
from your syringe to the waste tank.
7. If clog cannot be removed, replace DCM pump tubing by
removing C-clamp as well as tubing clamp in Fig. 2.2. When
changing tubing keep tubing taught against pinch rollers, then
tighten tubing clamp.
k

Home
Troubleshooting Section 3
Fig 3.1 Flow Cell Area**

Checking for clog in waste line Black line to waste during run
1. While performing drain and fills (prime for FCB), and fill. Pressurizes during
drain Remove here in
observe flow cell area below viewing orifice (fig 3.1), accordance with step 3.
and the waste line going to the waste tank (fig. 2.3). You should see
fluid drain from the flow cell to the waste tank during the Viewing
drain cycle (first half of the prime cycle). You should see fluid orifice
fill the flow cell and the waste line during the fill. Check that the rate
of fluid flow into the waste tank increases when the mode changes
from FILL(PRIME) to RUN. If you observe the above the problem
may be gone. Try running calibration particles. If the above is not
Check here to observe
observed proceed with step 2. flow cell draining and
2. Remove clear silicone tubing from pinch valve (fig 3.2) to see filling
if this corrects problem. If problem is corrected you may have Blue line to
waste during
a problem with the pinch valve or the electronics that control it. drain
3. If draining is not happening try removing the black line
(fig 3.1) from the top of the flow cell and check to see if it
is blowing air during the drain cycle. If the line is blowing
air check for clogs by following the blue line (fig 3.1) to the
orange line to the waste tank (fig 2.3). Chances are the clog
is happening at one of the quick disconnect fittings between
the flow cell and waste tank.
Fig 3.2 Fluidics Box (Facscan)

Remove Hydrophobic
silicone tubing filter for air line
from pinch
valve here
IAW step 2. Pressure transducer

*Pictures are sub-assemblies of the

Facscan .

** Follow manufactures safety precautions

when viewing flow cell with optics cover
removed

Home
Troubleshooting Section 4 Fig. 4.1 Laser Shutter/Flow cell

Checking Instrument for a NOT READY condition

The instrument will have a NOT READY condition for one of
Observe laser light at these places
the following reasons:
1. First Five Minutes of operation
2. Low laser power
3. Sheath tank empty
4. Waste tank full
Before proceeding with this step wear laser safety glasses.
To check to see if there is a laser output (see fig. 4.1). If
laser is light is observed proceed, if not call for
assistance.
Check sheath and waste tank status in the instrument
status page of your software. If sheath tank is greater than
half-full and waste tank is less than half full proceed. If
they are not, fill sheath tank and empty waste tank.
If sheath status is empty, even though the tank is full
disconnect the sheath level sensor from J69, then short
together the contacts at J69 (Fig. 4.2) with a paper clip or Lift laser shutter here
small piece of wire. If the sheath status is now OK or Full
then there is a problem with the sensor. If the sheath
status is still empty, chances are there is an electronic
problem. Call for assistance.
If the waste status is full, even though the tank is Fig. 4.2 Sheath/Waste Tanks
empty, disconnect the waste probe from J70. If the
status goes to OK or empty, then the waste probe is Short together the contacts of
bad. If the status doesn’t change, chances are it is an J69.
Disconnect the waste probe from
electronic problem. Call for assistance. Saline filter air bleed off J70 as shown below.

*Pictures are sub-assemblies of the

Facscan .

** Follow manufactures safety precautions

when viewing flow cell with optics cover
removed Home
Troubleshooting Section 5
Fig. 5.1 fluidics compartment (viewed from right side)
Checking Instrument when in a STANDBY condition
The instrument has two modes of STANDBY (STBY).
Hydrophobic filters
Soft STBY: This is when the instrument is manually set to RUN Blue: sheath tank air
but stays in STBY. Laser power will decrease and sheath fluid Green: sample
pressure air
will stop flowing after an approximately 10-sec. delay. This can
be caused by of one of the following reasons:
1. Sample arm pushed aside
Solution: push arm under tube
2. Sample tube cracked
Solution: transfer sample to new tube
3. Bal-seal worn
Solution: change Bal-Seal (see Fig 5.2 for assistance in
changing)
4. Sheath tank not pressurized (see fig.1.1)
Solution: change tank, level sensor cap, check vent
5. Sample pressure air leak in a place other than those listed
above
Solution: Check green air lines, change hydrophobic filters.
See fig 3.2 and 5.1 for locations of filters.
Hard STBY: This condition is set by manually selecting STBY
on the mode selector switch. When in STBY, sample pressure is
vented, laser power decreases, and sheath fluid stops flowing.

The following steps were photographed on an instrument that had been fully decontaminated prior to refurbishment. Manufacturer recommends the
wearing of protective gloves while performing the following steps.
Fig. 5.2 Changing the Bal-seal (steps 1-5)

Step 1. Remove drip Step 2. Remove Bal-seal Step 3. Attach Bal-seal to SIP, Step 4. Bal-seal shown installed Step 5. Reinstall drip tube
tube and retaining nut (shown removed) Attach at an angle, and then in place and retaining nut
push lower side of bal-seal
into place

Home
Troubleshooting section 6

No sample flow rate while instrument is in a READY condition

One or more of the following reasons can cause no flow rate while in READY.
1. SIP is clogged
Solution: Run cleaning solution on high for five minutes, clean SIP with cleaning wire See Fig 6.1
Be CAREFUL not lose the cleaning wire in the flow cell, bend it over ¼” at one end.
2. Sample signal is not above the threshold value
Solution: Check threshold value and parameter and ensure that sample has a signal above the threshold value.
3. Sheath fluid is not flowing properly
Solution: Perform drain/fill (prime). Ensure that there is not an air bubble trapped in the sheath filter ( see fig. 7.1). If
there is an air bubble bleed off air in saline filter. Monitor the flow of fluid to the waste tank. (fig. 2.3) If fluid is not
flowing to the waste tank refer to troubleshooting section 3.
4. Sample tube is not pressurized sufficiently. The sample tube may have enough pressure to get a READY or
RUN condition, yet, this pressure may not be high enough to put the sample into the flow of sheath fluid
Solution: Check the sample voltages in the status page of your software. They should be approximately; HI: 5.95,
MED: 6.11, LOW: 6.33 and STBY: 10.23. If these voltages are not correct try troubleshooting the sample air lines The following steps in Fig 6.1 were
photographed on an instrument that had
(Green lines), the differential pressure regulator (fig 2.2)or check the pressure transducer. (fig 3.2) if they are
been fully decontaminated prior to
correct, you may have a clogged waste line see fig 3 or flush through the black line. refurbishment Manufacturer recommends
the wearing of protective gloves while
performing the following steps.

Fig 6.1 Cleaning the Sample injection Probe (SIP) with a cleaning wire

Step 6. Replace drip tube by tightening drip tube

Step 1. De-pressurize sheath tank, place instrument in Step4. Carefully insert cleaning wire into bottom of retaining nut ¼ turn past o-ring contact
STBY, then remove the drip tube & retaining nut SIP. Insert wire slowly to prevent wire from bending.

Home
Troubleshooting Section 7
Fig. 7.1 Exploded view of flow cell viewing orifice
Instrument is failing daily QC procedure
1. Before proceeding verify particles are not expired, sheath fluid is
and tubes are clean and you have tried a new batch of beads.
2. Instrument is failing FSC sensitivity test. This is caused by a
high signal to noise ratio detected by the FSC detector.
Solution: first perform a few drain and Fills (primes), recheck. If Exploded view of viewing
still failing try monthly cleaning procedure, recheck. If still failing orifice
perform flow cell flush with syringe and 50% bleach(see fig. 7.2).
Laser
3. Instrument failing SSC sensitivity test. This is caused by a
high signal to noise ratio detected by the SSC detector. 2nd Laser Flow
Solution: Bleed off excess air in saline filter (fig.4.2), recheck. If Channel
still failing perform monthly cleaning, recheck. If still failing
Check for
perform flow cell flush with syringe and 50% bleach(see fig. 7.2). Bubbles here
4. Instrument failing Fluorescence sensitivity test. This is
caused by a high signal to noise ratio detected by the FL(X )
detector. cells
Solution: If beads are good, check for bubble in flow cell (fig. 7.1
SIP clogged or clog in the waste lines (Sec. 3). If the flow cell is
bubble free, and the SIP and waste lines are not clogged suspect
poor optical alignment.

Before performing the steps in figure 7.2, drain flow cell (FACScalibur press prime, wait for flow cell to drain ,
Fig. 7.2 Flushing flow cell with syringe then put instrument in STBY), de-pressurize sheath tank, then turn instrument off.

Step 1. Remove optics cover Step 2. Remove the drain line (Black line) from
the barb fitting on top of the flow cell

Home
 The following steps in Fig 7.2 were photographed on an instrument that had been fully decontaminated prior
to refurbishment. Manufacturer recommends the wearing of protective gloves and clothing while performing
Fig. 7.2 Flushing flow cell with syringe the following steps.
(Cont.)
Before performing the steps in figure 7.2, drain flow cell (FACScalibur press prime, wait for flow cell to drain ,
then put instrument in STBY), de-pressurize sheath tank, then turn instrument off.

Step 4. Connect a syringe with 50% bleach

solution to barb fitting on top of the flow cell

Step 8. Reconnect the black waste line to the barb

fittting on top of the flow cell.
Home