Advanced Instruments Anoxomat Mark II CTS User manual

Anoxomat® Mark II CTS
user’s guide

2Anoxomat Mark II CTS User’s guide
Table of contents
Safe use 4
Symbol conventions 4
General cautions 5
FCC requirements 5
Foreword: Intended use 6
Chapter 1
Installation and setup 7
1.1 Find a location for the instrument 7
1.2 Obtain additional items 7
1.3 Unpack the instrument 7
1.4 Install the primary (standard) gas supply 8
1.5 Install the recipe printer (optional) 9
1.6 Connecting to a computer or network (optional) 9
1.7 Power up the instrument 9
1.8 How to input data 10
1.9 Setting up the instrument 10
1.10 Standard gas mixture 12
1.11 Registration setup (optional) 13
1.12 Activating the printer (optional) 15
1.13 Activating the data interface (optional) 15
Fig. 1.1 Anoxomat Mark II CTS and accessories 8
Fig. 1.2 Tube and gas connections 9
Fig. 1.3 Power entry and on/o switch 9
Fig. 1.4 Red touch screen protection label 9
Fig. 1.5 Main screen 10
Fig. 1.6 Setup code 10
Fig. 1.7 Main setup 10
Fig. 1.8 Gas connection setup 10
Fig. 1.9 Edit gas mixture 11
Fig. 1.10 Setup language 11
Fig. 1.11 Set date/time 11
Fig. 1.12 Unlock registration code 13
Fig. 1.13 Registration 13
Fig. 1.14 Jar setup 13
Fig. 1.15 Add user 14
Fig. 1.16 Registered user 14
Fig. 1.17 Connect printer 15
Fig. 1.18 Choose printer 15
Fig. 1.19 Enter fixed ip address 15
Fig. 1.20 Set IP address of network card 16
Table 1.1 Anoxomat Mark II CTS packing list 7
Table 1.2 Gas supply mixtures and jar composition results 12
Chapter 2
Instrument operation 17
2.1 Function of major components 17
2.2 Operating procedure 17
2.3 Process report 18
2.4 End of recipe 19
2.5 Quality Assurance program 19
2.6 Changing the Quality Assurance level for one run 20
2.7 Changing the default Quality Assurance
level for a recipe 20
Fig. 2.1 Connect jars 18
Fig. 2.2 Process report 18
Fig. 2.3 Active recipe 18
Fig. 2.4 Set quality assurance level 20
Fig. 2.5 Program recipes 20
Fig. 2.6 Edit recipe 20
Chapter 3
Optional functions 21
3.1 Barcode scanner 21
3.2 Registration Input screen 21
3.3 Pre-programmed recipes 22
3.4 Additional jar connections 22

3
Anoxomat Mark II CTS User’s guide
3.5 Additional gas connections 22
3.6 User programming function 23
3.7 Activating pre-programmed or user-defined recipes 25
3.8 Thermal/dot matrix printer 25
3.9 Data interface 26
Fig. 3.1 Project details 21
Fig. 3.2 Jar content 21
Fig. 3.3 Program recipes 23
Fig. 3.4 Unlock programming 23
Fig. 3.5 New recipe 23
Fig. 3.6 Define QA and maximum evacuation levels 24
Fig. 3.7 Printout 25
Fig. 3.8 Printout with registration input 25
Fig. 3.9 Print last recipe 25
Fig. 3.10 Anoxomat web page 26
Fig. 3.11 Generated CSV file 26
Fig. 3.12 Menu bar 26
Fig. 3.13 Get recipes form Anoxomat 26
Fig. 3.14 Overview of filtered recipes 27
Fig. 3.15 Filter page 27
Fig. 3.16 Anoxomat statistics report 27
Table 3.2 Primary and one secondary gas supply 22
Table 3.2 Primary and two secondary gas supplies 22
Chapter 4
Maintenance 28
4.1 Maintaining the Anoxomat 28
4.2 Maintaining jars 28
Fig. 4.1 Cracked jar 29
Fig. 4.2 Cracked jar 29
Chapter 5
Troubleshooting and service 30
5.1 Service and maintenance cautions 30
5.2 Obtaining service 30
5.3 To return an instrument for repair or replacement 31
5.4 Troubleshooting checks 31
5.5 Process report errors 31
5.6 Hardware test program 31
5.7 Fuse replacement 31
Fig. 5.1 Process report 31
Fig. 5.2 Hardware test 31
Appendix A
Troubleshooting table 32
Appendix B
Parts and accessories 36
Appendix C
Product specifications 38
Appendix D
Regulatory notices 39
Appendix E
Warranty and warranty duties 41
Appendix F
Supplemental RS-232 information 44
Appendix G
Symbol definitions 45
Appendix H
Product disposal and recycling 47
Appendix I
Service log 48

4Anoxomat Mark II CTS User’s guide
Safe use
To reduce the risk of bodily injury, electric shock, fire, and damage to your instrument, please read and observe the
precautions in this User’s Guide.
If the product is used in a manner not in accordance with the equipment design, operating instructions or manufacturer’s
recommendations, the operation of the product may be impaired to the extent that a safety hazard is created.
Do not attempt to perform electrical work if you are not fully qualified. This manual is not a substitute for electrical training.
Symbol conventions
The exclamation point within an equilateral triangle is intended to alert the user to the presence of important
operating and maintenance (servicing) instructions in the literature accompanying this product.
The lightning flash with arrowhead symbol within an equilateral triangle is intended to alert the user to the
presence of uninsulated dangerous voltage within the product’s enclosure that may be of sucient
magnitude to constitute risk of electric shock to persons.
The static symbol within an equilateral triangle is intended to alert the user to the presence of internal
components that could be damaged by static electricity.
This static symbol is intended to alert the user to the presence of a specific component that could be
damaged by static electricity.
This symbol indicates the presence of alternating current (AC).
This symbol indicates the presence of a fuse.
This symbol indicates the presence of protective earth ground.
This symbol indicates the power is ON.
This symbol indicates the power is OFF.
Additional symbol definitions are available in Appendix F.

5
Anoxomat Mark II CTS User’s guide
Safe use
General cautions
• This product should be operated only with the type of
power source indicated on the product’s electrical
ratings label. Refer to the installation instructions
included with the product.
• If the power cord provided is replaced for any reason
or if an alternate cord is used, the cord must be
approved for use in the local country. The power cord
must be approved for the product’s listed operating
voltage and be rated at least 20% greater than the
volt-ampere (VA)ratings marked on the product’s
electrical ratings label. The cord end that connects to
the product must have an IEC 60320 connector.
• Plug the product into an approved grounded electrical
outlet. Exposure to AC voltage could lead to electric
shock, burn or electrocution. Please be aware of any
exposure of AC voltage in the power cord.
• Do not disable the power cord’s grounding pin.
• If an extension cord or power strip is used, make sure
that the cord or strip is rated for the product, and that
the total ampere ratings of all products plugged into
the extension cord or strip do not exceed 80% of the
cord’s or strip’s rating limit.
• Route power cords so that they will not be walked on,
tripped on, or pinched by items placed upon or
against them. Pay particular attention to the plug,
electrical outlet, and the point where the cord exits
the product.
• Do not pull on cords and cables. When unplugging
cords or cables, grasp the corresponding connector.
• Do not install or use this product in any area subject
to extreme short-term temperature variations, or
locations that exceed the specified operating
environment temperatures.
• Never use this product in a wet area.
• To avoid injury or fire hazard, do not operate this
product in an explosive atmosphere.
• Do not install or use the product on an unstable,
non-level work surface.
• Do not operate this product with the covers removed
or unsecured.
FCC requirements
WARNING: Changes or modifications to this unit
not expressly approved by the party responsible for
compliance could void the user’s authority to
operate the equipment.
If you have any questions or problems regarding the
operation of this instrument, please contact our technical
support department:
Advanced Instruments
Two Technology Way
Norwood, MA 02062, USA
Phone: [phone]
Fax: [phone]
Web: aicompanies.com or anoxomat.com
Email: [e-mail] or [e-mail]
Technical support/product service
Phone: U.S. and Canada 800-225-4034
[phone]
Email: [e-mail]
Customer service/orders
Phone: [phone] or [phone]
Fax: [phone]
Email: [e-mail]
This equipment has been tested and found to comply
with the limits for a Class A digital device, pursuant to
Part 15 of the FCC Rules. These limits are designed to
provide reasonable protection against harmful
interference when the equipment is operated in a
commercial environment. This equipment generates,
uses, and can radiate radio frequency energy and, if not
installed and used in accordance with the instruction
manual, may cause harmful interference to radio
communications. Operation of this equipment in a
residential area is likely to cause harmful interference in
which case the user will be required to correct the
interference at his own expense.

6Anoxomat Mark II CTS User’s guide
Foreword
Intended use
The Advanced Instruments Anoxomat Mark II CTS system is an automated system for creating an anaerobic,
microaerophilic, capnophilic, or user-defined atmosphere in an anaerobic jar. The condition is created by evacuating a jar
and filling it again with a (oxygen-free) gas mixture, according to the Method of McIntosh and Fildes.
The Advanced Instruments Anoxomat Mark II CTS system controls this process by means of an embedded computer, and
performs various quality assurance tests to ensure that conditions for optimum bacterial growth are precisely met.

7
Anoxomat Mark II CTS User’s guide
Installation and setup
Chapter 1
1.1 Find a location for the instrument
When choosing a location for your Anoxomat, be sure to
meet the following criteria.
Adequate space
• The dimensions of the instrument are 12.6 × 21.7 × 10.8
inches (32 × 55 × 28 cm). Be sure to keep your
workplace free of debris and allow 6 inches (15 cm) of
clear space on each side of the instrument.
Electric outlet availability
Your instrument will need to operate within five feet
of a properly grounded, three-prong electrical outlet
capable of continuously supplying 2 amperes at 220V and
5 amperes at 110V. If the instrument is not grounded
properly, its operation may be impaired and a safety
hazard may exist. Therefore, be sure to test the outlet and
record the results before operating your instrument.
1.2 Obtain additional items
To install the Anoxomat, you will need to obtain the
following items:
• Adjustable wrench to tighten the dual stage regulator.
• Adjustable-joint pliers to tighten the gas tube clamps.
• Gas cylinder containing appropriate anaerobic mixture
• Dual stage regulator (1.8 bar). Refer to Section 1.4.
1.1 Unpack the instrument
In order to set up your instrument properly, it is important that you read and follow the steps in this section.
Please follow these steps carefully and be sure to read Chapter 2—Instrument Operation before attempting to run
your instrument.
Quantity Description
1 The Anoxomat Mark II CTS
1
Parts package
• Gas tube(s)
• Jar tube plug
• Seven gas tube clamps
• Soft-touch pen
• Penholder
1
USB stick containing
• Quick Installation Guide
• Quick Usage Guide
• User’s Guide
• Data Interface spreadsheet template
1 Warranty Card
1 Customer Satisfaction Card
1 AC Line Cord
Table 1.1: Anoxomat Mark II CTS Packing List

8Anoxomat Mark II CTS User’s guide
Chapter 1 Installation and setup
Accessories and optional parts
• Jar
• Petri dish holder
• Catalyst
• 1 Recipe printer (optional, if ordered)
• 1 Barcode scanner (optional, if ordered)
To unpack your Anoxomat, take the following steps.
1. Carefully unpack your Anoxomat, accessories and
supplies and inspect them for shipping damage. Use
the enclosed packing list to verify that all items have
been received.
2. Save your Anoxomat’s shipping boxes and packaging
material in case future transport of the instrument
becomes necessary.
3. If any item on the packing list appears to be missing
from your shipment, please search carefully through
and under all packing materials. If the item is not
found, notify your receiving department immediately.
Advanced Instruments can only be responsible
for items reported missing within 10 days of a
shipment’s arrival.
4. If you receive any damaged items, save the cartons
and packing material those items came in for
inspection by the insurer. The dealer, and Advanced
Instruments must be notified within 24 hours in order
for your warranty and insurance to apply. Have the
transportation company inspect items, fill out a
“Report of Concealed Damage,” and file your claim.
Then, notify Advanced Instruments immediately for
repair or replacement.
5. Fill out the warranty card enclosed. Mark the
appropriate boxes if you wish to receive additional
information. Mail or fax to 781-320-8181.
1.4 Install the primary (standard) gas supply
For creating standard anaerobic and/or
microaerophilic conditions, one gas cylinder should
be connected with a standard gas mixture used
for anaerobic bacteria cultivation, as well as for
microaerophilic bacteria cultivation (see Standard Gas
Mixture, later in this chapter).
The regulator to be used with the Anoxomat, should
have the following criteria:
1. Reverse thread for mixed gases
2. Dual-stage
3. Reads 0–3.45 bar (0–50 psi).
4. Required hose-barb fitting: 8mm (1/4 or 3/8 in).
5. Capacity max. 5 m3/ hr (176 ft3/hr).
Regulators connected with the Anoxomat shall comply
with safety standards. The gas cylinder should be
equipped with a CGA350 fitting on the tank, and using
the recommended regulator, the Anoxomat working
pressure should be at 1.75 bar ± .15 bar 25.5 ± 2 psi.
The gas tube used with the Anoxomat has an 8mm
inner diameter (3/8 in), and a pressure rating of 20
bar (290 psi).
Fig. 1.1: Anoxomat Mark II CTS and accessories

9
Anoxomat Mark II CTS User’s guide
Chapter 1 Installation and setup
Follow the Quick Instruction Guide included with the
Anoxomat to install the primary gas supply:
1. Mount the reducing valve on the gas cylinder
using the adjustable wrench. Tighten the reducing
valve per manufacturer’s recommendations to avoid
leakage of gas. Set the pressure on the reducing valve
gas pressure to zero.
2. Using tube clamps on each end, connect the gas
tube to the reducing valve and the gas input #1
(Fig. 1.2) of the Anoxomat. Use pliers to tighten the
gas tube clamps.
3. Open the gas cylinder’s main supply and set the
reducing valve gas pressure to. 1.75 ± .15 bar.
1.5 Install the recipe printer (optional)
Following the instructions included with the printer:
1. Connect the printer cable to the RS232 socket on the
bottom of the Anoxomat.
2. Install the roll of printer paper.
3. Connect the printer power supply assembly.
See instructions for Activating the Printer,
later in this chapter.
1.6 Connecting to a computer or network (optional)
If your Anoxomat includes a data interface to a computer
or network:
• Use a “cross-link” Ethernet cable to connect
the Anoxomat directly to the network card of
the computer.
• Use a standard patch cable to connect to a network.
See instructions for Activating the Data Interface, later in
this chapter.
1.7 Power up the instrument
Power up the Anoxomat in the following manner:
1. Connect the power cord to the Anoxomat (Fig. 1.3) and
the power outlet.
2. Remove and set aside the red protection label
(Fig. 1.4) from the touch screen.
Fig. 1.2: Tube and gas connections
Fig. 1.3: Power entry and on/off switch
Be sure to keep the red label in a safe place as it contains
Anoxomat configuration access codes.
The red protection label contains important
information and setup codes for the Key Operator, and
should be stored in a safe place. See Fig. 1.4.
Fig. 1.4: Red touch screen protection label

10 Anoxomat Mark II CTS User’s guide
Chapter 1 Installation and setup
3. Turn on the power switch and wait for the Main screen
display (Fig. 1.5). The Anoxomat is equipped with a
touch screen that responds to the soft-touch pen
supplied with the instrument or the tips of your
fingers. The touch screen may not respond well if you
press with the flat of your finger. Never use sharp
objects, pens, pencils, or anything that would leave a
mark on the screen.
1.8 How to input data
When programming or changing settings in the
Anoxomat, you will be required to enter data on an input
line using an on-screen keyboard. Using the soft-touch
pen or your fingernail, tap in the input line to position a
blinking cursor, and a keyboard will appear.
1.9 Setting up the instrument
This section is restricted for use by the Supervisor , who
is required to enter the Set-up Code from the red label
(Fig. 1.4) before defining or changing settings.
1. Press Setup. The setup code screen displays with
keyboard (Fig. 1.6).
2. Enter the Setup Code from the red label (Fig. 1.4) and
press Ok. The main Set-up screen displays (Fig. 1.7).
Setup gas connection(s)
The Anoxomat allows a maximum of three gas supply
connections. For each gas connection, you need to
specify the gas mixture on the Setup screen.
For Gas #1, select the gas composition of your gas from
the corresponding pull-down menu (Fig. 1.8). If available,
and you are connecting more than one gas supply,
specify each gas composition in the same manner. See
Standard Gas Mixture, later in this chapter.
Fig. 1.7: Main setup
Fig. 1.8: Gas connection setup
Fig. 1.5: Main operation screen
Fig. 1.6: Setup code

11
Anoxomat Mark II CTS User’s guide
Chapter 1 Installation and setup
If your gas composition is not available from the pull-
down list, you can define the mixture by selecting “Other
gas-composition”, which will display the Edit Gas Mixture
screen (Fig. 1.9). Enter the required percentages in each
field and press Close to exit the screen and save changes.
If the second or third gas connection will not be used,
leave the field empty or select “None”.
Setup language
If you need to change the user interface language
of your Anoxomat, press Language on the setup
screen and select your preference from the
Language screen (Fig. 1.10).
Setup date and time
If your Anoxomat is equipped with a printer and/or is
using a data interface, the date and time of a process will
appear on the printout or in the database (Fig. 1.11).
To set the date and time, press Date/time on the
Setup screen. Using numbers, enter the date as
two-digit day, two-digit month, and four-digit year (e.g.,
30-04-2010 = April 30, 2010). Based on 24-hour clock,
set the time in two-digit hour and two-digit minutes
(e.g., 09-07 = 9:07 AM).
Exit Setup
Press Close to exit the Setup Menu and return to the
Main Operation Screen.
Fig. 1.9: Edit gas mixture
Fig. 1.10: Setup language
Fig. 1.11: Set date/time

Chapter 1 Installation and setup
12 Anoxomat Mark II CTS User’s guide
1.10 Standard gas mixture
The standard gas mixture could have a composition as
specified in the line “Primary gas supply” in Table 2
below, along with the resulting jar mixture using the
standard recipes.
You must use the primary gas connection (gas #1) for
your anaerobic gas mixture cylinder. Normally, the
secondary gas connection (gas #2) is used for the 100%
CO cylinder, and the third gas connection (gas #3) is
used for the H mixture cylinder.
WARNING: Gas mixtures with hydrogen greater
than or equal to 14% is considered flammable.
Gas mixtures with concentrations of oxygen above the
normal 21% atmospheric significantly increases the risk
of ignition and fire. Never use such hazardous gas
mixtures with the Anoxomat.
For other jar composition results, see Additional Gas
Connection section.
Hydrogen gas at 14% is considered flammable, therefore
it is recommended that any gas mixture should not be
purchased above such limit.
High concentrations of oxygen are a potential fire
hazard for operators. It is not recommended to use
Oxygen above 21% atmospheric air.
The Anoxomat processes the recipes independent of
the gases or gas mixtures used.
Gas composition O2CO2H2N2
Primary gas supply (alternative 1) – 10.0% 10.0% 80.0%
Standard microaerophilic recipe 6.0% 7.1% 7.1% 79.8%
Standard anaerobic recipe 0.0% 10.0% 10.0% 80.0%
Primary gas supply (alternative 2) ˜ 10% 5% 85%
Standard microaerophilic recipe 6.0% 7.1% 3.6% 83.3%
Standard anaerobic recipe 0.0% 10.0% 5.0% 85.0%
Table 1.2: Gas supply mixtures and jar composition results

Chapter 1 Installation and setup
13
Anoxomat Mark II CTS User’s guide
1.11 Registration setup (optional)
If you purchased the optional Registration feature, you
will receive a setup code that allows you to configure
your Anoxomat to record additional information on how
samples are processed, and who processed them (see
Chapter 3, Registration Input Screen). The details are
stored in the Anoxomat, can be printed with the optional
recipe printer, and can be transferred to a computer
using the optional data interface.
1. On the Setup screen, press Registration. The Unlock
Registration screen displays with keyboard (Fig. 1.12).
2. Enter the Registration Code from the red label
(Fig. 1.4) and press Ok. The main Registration screen
displays (Fig. 1.13).
3. Using the keyboard, enter the Lab ID and Dept. ID.
Jar setup
By configuring jar setup, the user will be prompted to
input data (e.g., Jar ID, contents of jars, job reference,
etc.) before each recipe is started.
1. On the Registration screen, press Jar Setup. The Jar
Setup screen (Fig. 1.14) displays a list of options and
corresponding check-boxes.
2. Using the soft-touch pen or your fingernail, select the
fields you want to include by tapping each box to
place a checkmark. If you checked a box by mistake,
tap again to remove the checkmark.
3. If you select the “Authorized by” check-box, a blank
line for signature/name authorization will appear on
the printout.
4. Press Close to save your settings and exit to the
Registration screen.
For each field selected, the user will have the option to
enter the respective information for each jar connected.
If no information is entered, a blank line will appear on
the printout. However, if the “Required” check-box is
selected, the user will be required to enter the
information.
Fig. 1.14: Jar setup
Fig. 1.13: Registration
Fig. 1.12: Unlock registration code
The ID separator is used when multiple patient plates are
scanned and processed in the jar.

Chapter 1 Installation and setup
14 Anoxomat Mark II CTS User’s guide
Register users
To limit access to the Anoxomat, user IDs can be
established to identify the technician before every recipe
is run.
1. On the Registration screen, press Register Users to
display the Register Users screen.
2. In the “Add user” section of the screen (Fig. 1.15), enter
the user’s full name as you want it to appear on the
printout and in the database.
3. Enter the user code that will be required for the user
to operate the Anoxomat. The user code will not
appear anywhere, but will need to be entered each
time a recipe is started.
4. Press Submit to add the name and code to the list of
registered users (Fig. 1.16).
5. Repeat steps 2–4 for each registered user.
6. To delete a registered user, select the entry from the
Registered Users list and press Remove.
7. Press Close to save your settings and exit to the
Registration screen. When you have finished
configuring Jar Setup and Register Users, press
Close to exit the Registration screen and return to
the Setup screen.
Fig. 1.15: Add user
Fig. 1.16: Registered User
As long as even a single user has been registered to use
the Anoxomat, the Anoxomat cannot be operated
without entering a correct user code.

Chapter 1 Installation and setup
15
Anoxomat Mark II CTS User’s guide
1.12 Activating the printer (optional)
If the optional thermal or dot matrix printer was
installed, you must activate the printer before use.
1. On the Setup screen, press Printer. The Connect Printer
screen displays with keyboard (Fig. 1.17).
2. Enter the Printer Code from the red label (Fig. 1.4) and
press Ok. The Printer screen displays (Fig. 1.18).
3. Choose the correct printer type and press Test Printer.
4. Select “Confirm Printout”, to automatically print out
the Anoxomat recipe cycle information without
prompting the user at the end of each cycle.
1.13 Activating the data interface (optional)
If you purchased the optional Data Interface feature, you
will need to setup and activate the software before you
can transfer data to a network or PC.
1. On the Setup screen, press Interface.
2. Enter the Data Interface Code from the red label
(Fig. 1.4) and press Ok. The Network Settings screen
displays (Fig. 1.19).
Connecting to a network
Use a standard patch cable (Ethernet Cable) to connect
to a network. Select “Obtain an IP address automatically”
and reboot the Anoxomat. The IP Address and Subnet
Mask will appear in the network settings.
Fig. 1.17: Connect printer
Fig. 1.18: Choose printer
Fig. 1.19: Enter fixed IP address
Only printers supplied by Advanced Instruments are
compatible with the Anoxomat system.

16 Anoxomat Mark II CTS User’s guide
Chapter 1 Installation and setup
Connecting directly to a PC
Use a “cross-link” Ethernet cable to connect the
Anoxomat directly to the network card of the PC.
Contact your system administrator for a range of IP
addresses to be used and enter a fixed IP address
(Fig. 1.19).
Set the IP address of the network card in your PC within
the same range (Fig. 1.20). Reboot the Anoxomat to
activate the connection. (See Chapter 3, Data Interface.)
Fig. 1.20: Set IP address of network card

17
Anoxomat Mark II CTS User’s guide
Instrument operation
Chapter 2
2.1 Function of major components
Operation of the instrument will be quicker and easier if
you become familiar with the locations and functions of
the components, systems and controls described below
before proceeding further.
Jars and Petri dish holders
Petri dish holders are available for all jars and
for the usual Petri dishes. Refer to Appendix B for
additional information.
Catalyst
The catalyst is clipped under the lid of the Standard jars,
or placed in the designated slot in the Ergonomic jar.
The Catalyst consists of a stainless steel sachet with
palladium-coated alumina pellets. Advanced Instruments
advises regenerating catalysts after every incubation to
avoid the use of ineective catalysts. The palladium
pellets can be inactivated by excessive moisture and HS;
therefore, they should be reactivated by heating the
sachet of pellets to 160˚C in a drying oven for 90
minutes. The regenerated catalysts can be stored at
room temperature in a clean, dry environment until ready
for use.
The catalyst should be renewed regularly because
irreversible degradation of catalytic activity takes place
(due to chemical binding with Sulfur ions). The end-of-
life period depends on the type of bacterium cultivated
or, more accurately, the HS production. Therefore, it
cannot be determined exactly how many incubation
cycles can be completed with one sachet.
2.2 Operating procedure
1. Place inoculated dishes, tubes, micro well plates, or
other samples in the jar using the Petri dish holder.
2. Add catalysts to jar for anaerobic bacterial cultivation.
It is also, recommended to use optical oxygen
indicator strip or appropriate QC plate in the jar.
3. Place the lid on the jar and slide the jar clamp over the
lid. Tighten (finger-tight only) the jar clamp screw. If
the ergonomic jars are used, close the clamps on each
side of the jar lid.
4. Connect the jars to the Anoxomat by pushing the jar
tube connector into the snap-shut coupling on the jar
lid, as shown in (Fig. 2.1). If the Jar tube connector
does not snap in place, pull the outer ring of the
snap-shut coupling downward.
5. Choose the appropriate recipe on the Main screen by
touching the microaerophilic or, the anaerobic button
or the saved recipe button (for any personalized
recipes). The button is highlighted when the recipe
is active.
6. For the standard microaerophilic and anaerobic
recipe, a standard quality assurance level has
been set as default. The Anoxomat automatically
enables this quality assurance level. To disable the
quality assurance setting, press Quality Assurance
enabled: level 1. The button will change to Quality
Assurance disabled. Details of the recipe are displayed
on the right hand side of the main screen (Fig. 2.3).
In order to run your instrument properly, it is important that you read
and adhere to the instructions in this section.
Maximum gas supply pressure to the Anoxomat
should never exceed 2 bar absolute.
Prior to use always check the jar for any cracks
or damage.
When catalyst reaches its end of life, it should be
disposed of in accordance with lab procedures and local
biohazard waste disposal regulations.

18 Anoxomat Mark II CTS User’s guide
Chapter 2 Instrument operation
The quality assurance level may be changed at any time
before a run begins, either to the default or for a single
run only. See Changing the Quality Assurance level.
7. Press the Start/Continue button located below the
touch screen.
2.3 Process report
During a recipe run and after it has finished, a
process report will display the following information
on the screen (Fig. 2.2):
• The recipe selected.
• If Quality Assurance was enabled and at which level.
• The status of the recipe (which cycle the Anoxomat is
in and which operation is currently performed).
• The results of the tests performed on each gas and jar
connection separately, and corresponding Quality
Assurance steps.
When an appears in the Connected column, it means
that the jar is under vacuum. Possibly, it was partly
processed and did not pass a QA test.
When a appears for one of the parts of the Quality
Assurance, this means that the jar has passed that
particular test.
A means that the jar failed on that specific step of
the Quality Assurance. In this case, the Anoxomat does
not process the jar any further. The jar may be
disconnected at that point. The Anoxomat continues
only with the jars that passed all Quality steps.
If a jar passed all steps of the Quality Assurance, it has
cycled the gas in the jar, and is ready to be disconnected
and placed in the incubator. A in the Ready column is
the indication that the process has been completed.
Fig. 2.2: Process report
Fig. 2.3: Active recipe
Fig. 2.1: Connect jars
It is recommended to always use the Quality Assurance
option during anaerobic and microaerophilic process to
avoid any failure or loss of patient samples.

19
Anoxomat Mark II CTS User’s guide
Chapter 2 Instrument operation
Gas-input test
When the Gas-input test fails, this means the pressure
supplied by the reducing valve to the Anoxomat is lower
than 1.6 Bar or higher than 1.9 Bar. Only the gas
connection needed for the specific recipe selected
is being tested.
Jar-leak test
When a connected jar fails the jar-leak test, this means a
leak has been detected in deep vacuum condition.
Seal-leak test
When a connected jar fails the seal-leak test, this means
a leak has been detected at near atmospheric pressure.
This normally means the seal between the lid and the jar
(rubber O-ring in the lid) is insucient.
Catalyst-activity test
When a connected jar fails the catalyst test, it means
that either the catalyst used is not active enough to
achieve and maintain an anaerobic atmosphere in the jar
during incubation or the gas mixture does not contain
enough Hydrogen. In case a appears during a
microaerophilic recipe, it means that a catalyst was
wrongly used in the jar.
2.4 End of recipe
As soon as a appears in the Ready column of the
respective jar, the jar is ready for incubation. It can be
disconnected.
Print recipe (optional)
If a printer is connected, you will be prompted to
print out the recipe just finished. The recipe can also
be printed out at a later stage. The software can be
personalized to automatically print without any
request on the main screen.
Disconnect and incubate
Disconnect the jar by pulling the outer ring of the
snap-shut coupling downward. The jar tube should snap
out of the coupling. This closes the snap-shut coupling
and maintains air tightness of the jar.
To leave the process report screen, press the Start/
Continue button. The Anoxomat returns to the Main
screen and is ready for the next job.
The last performed recipe stays active. This can be
checked in the “Active recipe” section (Fig. 2.3) on the
main screen.
2.5 Quality Assurance program
For the standard microaerophilic and anaerobic recipe, a
standard quality assurance level has been set as default.
The Anoxomat automatically enables this quality
assurance level. To disable the quality assurance setting,
press Quality Assurance enabled: level 1. The button will
change to Quality Assurance disabled.
Levels of quality assurance
The levels of the quality assurance test determine the
length of the seal leak test and the catalyst test.
Level Description
1Gas input test, jar leak test seal leak test and/or
catalyst test* (60”)
2Gas input test, jar leak test seal leak test and/or
catalyst test* (90”)
3Gas input test, jar leak test seal leak test and/or
catalyst test* (120”)
4Gas input test, jar leak test seal leak test and/or
catalyst test* (150”)
5Gas input test, jar leak test seal leak test and/or
catalyst test* (180”)
0Disabled as default
*If a microaerophilic recipe is selected, the quality assurance level only influences the
duration of the seal leak test, because no catalyst is needed.
Length of catalyst test/seal leak test
Under certain circumstances, users might prefer to
increase or decrease the catalyst or seal test time.
• Anaerobic: In case of a new and well-reactivated
catalyst, the test may pass quicker than the selected
test level, thus saving time.
• Microaerophilic: The test will continue the full time of
the chosen level.
In case of older (slower, but with enough activity)
reactivated catalysts, a longer testing time may be
necessary to have the catalyst pass the test. You can still
work with these catalysts; however, it is an indication to
order new catalysts soon.
Hold the black tube with your other hand, when
disconnecting from the jar.
The quality assurance setting should be enabled before
any recipe is started in order to be active for the cycle.

20 Anoxomat Mark II CTS User’s guide
Chapter 2 Instrument operation
2.6 Changing the Quality Assurance level
for a specific test
To override the standard quality assurance level of the
active program:
1. Press the Set Quality Assurance level button on the
Main screen after selecting the recipe.
2. Change the quality Assurance level.
The chosen level of the quality assurance test is
displayed on the Main screen, on the process report, on
the printout and CSV file using the Data Interface
(optional accessories).
The quality assurance level resets to the default setting,
once the test is complete and the recipe reselected.
2.7 Changing the default Quality Assurance level
for a recipe
To change the default setting for the standard quality
assurance level:
1. Press the Program recipes button on the bottom
of the Main screen to display the Program Recipes
screen (Fig. 2.5).
2. Select the recipe for which you want to change the
default quality assurance level. The Edit Recipe screen
(Fig. 2.6) will display the settings.
3. Select the new default level from the QA Level
drop-down box.
4. Press Close to save the settings and return to the
Program Recipes screen, and press Close again to
return to the Main screen. The default for the selected
recipe has been changed.
Fig. 2.4: Set quality assurance level
Fig. 2.5: Program recipies
Fig. 2.6: Edit recipe