Cytomat 2

The Cytomat 2 is Thermo’s most compact incubated plate store: random-access storage with a controlled atmosphere inside. Of the four Cytomat devices Revolution drives, it is the only one with atmosphere and shaking control exposed to a schedule — the Cytomat 10C, Cytomat 24 (PH) and Cytomat 6000 are larger ambient stores without those operations.

At a glance

Capacity	56 × 1536-well plates, 42 × 96-/384-well, 20 × deep-well plates
Temperature	Ambient +10 °C to 50 °C
Humidity	Up to 95% r.H.
Shaking	Two independently driven stacks, 50–1200 rpm
Revolution control	Read/write temperature, humidity, CO₂ and O₂; per-stack shaking; the store’s transfer mechanism; self-scan inventory

Specifications

Thermo Fisher publishes the following for the Cytomat 2 C-LiN, the incubated variant this driver targets.

Temperature range	Ambient +10 °C to 50 °C
Humidity	Controlled, up to 95% r.H.
CO₂ range	0–20 Vol. %

Capacity depends on plate type, not just the model: the same unit holds 56 1536-well plates but only 20 of some deeper types, because plate height is what governs how many shelves fit.

Supported methods

Environment

• Get / set temperature
• Get / set CO₂
• Get / set oxygen
• Get / set humidity

Read as well as write, on all four. That matters for an unattended run: a schedule can verify the atmosphere is what it should be before committing cells to it, rather than assuming the set point was reached.

Shaking

• Set shake mode — record the desired state (Enabled, Disabled, or NotSupported if no shaker is fitted) without touching the hardware
• Turn shake on / turn shake off — set the same state and actuate it immediately
• Get / set stack 1 frequency, get / set stack 2 frequency — 50–1200 rpm, default 500 rpm

The two stacks have independently settable frequencies, so different plates in the same store can be agitated differently. Thermo notes that frequencies above 800 rpm may cause resonance — back off if you encounter it.

Shaking is paused automatically whenever a plate is stored or retrieved, then restarted afterward if it was enabled and plates remain to shake. If the shaker fails to start, the driver retries with a re-initialise up to three times before raising a warning — no separate “initialise shaker” operation exists to call by hand.

Plate movement and transfer mechanism

Storing and retrieving a plate is driven by the scheduler’s normal pick/place mechanism, the same as any other random-access store — there is no separate “load” or “unload” command to call. The underlying transfer mechanism is also exposed step by step, for commissioning, teaching and fault recovery:

• Extend shovel / retract shovel
• Move height motor to above / below store location
• Move to wait position
• Move transfer station to basic position / to position 2 — only meaningful where a transfer station is fitted (HasTransferStation device property)
• Open / close automatic lift door
• Initialise hardware

The Cytomat 2 has no turntable and no carousel — it is a small, two-column store, so it doesn’t carry the turntable/carousel rotation operations that the larger rotary Cytomat models expose.

Inventory and status

• Start self scan / Start self scan (full)
• Show status / Show extended status
• Show extended options settings

A self-scan rebuilds the inventory from what is physically present. Run one after any manual loading, or Revolution’s view of the contents is only as good as its bookkeeping.

Integration

Prerequisites

• The store must be reachable from the Revolution host.
• Atmosphere set points must be reached before cells go in — set, then read back to confirm, rather than assuming.
• Plate type must suit the store’s shelf pitch; capacity depends on plate height.
• Where the unit has no shaker fitted, set the shake mode to NotSupported so plate transfers don’t attempt to actuate it.
• Run a self-scan after manual loading.

Other Cytomat variants exist in the driver but are not currently enabled — including the Cytomat 48 and the Cytomat 2C LiN Under Bench. If you need one of those, or another model in Thermo’s range, get in touch: it is a matter of enabling and commissioning rather than writing a driver.

If you need more of this instrument driven from a schedule, get in touch — the driver is extended on demand.

Operations

These are available from a Run Device Operation step.

Close Automatic Lift Door

Closes the unit's automatic lift door and waits for the unit to report the move complete, failing if that has not happened within ten seconds. Show Status reports whether the door is open, so it can be used to confirm the result.

Extend Shovel

Extends the shovel from its retracted position, at whatever height and rotation the mechanism is currently holding, and leaves the other axes where they are. The shovel stays extended until Retract Shovel is run, and the step fails if the move is not reported complete within ten seconds.

Get Co2

Retrieves the current Set Point and Actual Co2 percentage and displays in Revolution console.

Get Humidity

Retrieves the current Set Point and Actual Humidity percentage and displays in Revolution console.

Get Oxygen

Retrieves the current Set Point and Actual Oxygen percentage and displays in Revolution console.

Get Stack1 Frequency

Reads the current shaking frequency of stack 1 in rpm and shows it in the Revolution console.

Get Stack2 Frequency

Reads the current shaking frequency of stack 2 in rpm and shows it in the Revolution console.

Get Temperature

Retrieves the current Set Point and Actual Temperature (deg C) and displays in Revolution console.

Initialise Hardware

Clears any latched error flags and runs the unit's own initialisation sequence, waiting for the unit to report that it has finished and failing if that takes longer than three minutes. Bringing the device online does not run this sequence, so this is the step to use after a power cycle or after clearing a fault.

Move Height Motor To Above Store Location

Drives the height axis to above the level of the given store location and leaves it there; nothing else moves and no labware is picked or placed. The device must be initialised and not part way through a self scan, and Move Height Motor To Below Store Location makes the matching move to below the location.

Parameter	Type	Default	Description
Store Location	int	—	The store location the height axis moves to, identified by its number in this unit's layout rather than by a height. The axis stops above that location and no labware is picked, placed or recorded.

Move Height Motor To Below Store Location

Drives the height axis to below the level of the given store location and leaves it there; nothing else moves and no labware is picked or placed. The device must be initialised and not part way through a self scan, and Move Height Motor To Above Store Location makes the matching move to above the location.

Parameter	Type	Default	Description
Store Location	int	—	The store location the height axis moves to, identified by its number in this unit's layout rather than by a height. The axis stops below that location and no labware is picked, placed or recorded.

Move To Wait Position

Moves the mechanism to its wait position inside the unit, close to the transfer station. Placing labware on this device moves the mechanism there first, so this step returns it to the same position without moving any labware.

Move Transfer Station To Basic Position

Moves a fitted transfer station to its basic position, position 1, which is where the unit loads labware onto it and takes labware off it. Store and retrieve steps move it there themselves, and a transfer station that is already in the basic position is reported as success rather than an error.

Move Transfer Station To Position2

Moves a fitted transfer station to position 2, the position it is left in at the end of a retrieve so that labware on it can be picked. A transfer station that is already in position 2 is reported as success rather than an error.

Open Automatic Lift Door

Opens the unit's automatic lift door and waits for the unit to report the move complete, failing if that has not happened within ten seconds. The device must be initialised and not part way through a self scan for this step to run.

Raise Error

Makes this device report a failure on demand: the step fails with an error naming the device, and the operator is offered the usual error recovery choices. No command reaches the instrument and nothing moves, and the failure is raised in simulation as well as on a real system, so this is the step to use when rehearsing how a schedule handles a device failure.

Retract Shovel

Retracts the shovel so that it is clear of the store positions, leaving the other axes where they are. The unit retracts the shovel itself at the start of a self scan, and the step fails if the move is not reported complete within ten seconds.

Set Co2

Sets the incubator's target carbon dioxide level as a percentage, to one decimal place. The step sends the setpoint only; the level measured in the chamber is reported separately and is not checked here.

Parameter	Type	Default	Description
Carbon Dioxide	double	—	Target carbon dioxide level as a percentage. The value is sent to the incubator to one decimal place.

Set Humidity

Sets the incubator's target humidity as a percentage, to one decimal place. The step completes once the incubator has accepted the setpoint, not once the chamber has reached it.

Parameter	Type	Default	Description
Humidity	double	—	Target humidity as a percentage. The value is sent to the incubator to one decimal place.

Set Oxygen

Sets the incubator's target oxygen level as a percentage, to one decimal place. It is applied whatever the incubator is currently doing, and the chamber then moves towards the new setpoint.

Parameter	Type	Default	Description
Oxygen	double	—	Target oxygen level as a percentage. The value is sent to the incubator to one decimal place.

Set Shake Mode

Records whether this incubator should be shaking, without starting or stopping the shaker now. The recorded mode is applied the next time a plate is stored or retrieved, so use Turn Shake On or Turn Shake Off to act on the shaker straight away.

Parameter	Type	Default	Description
Shake Mode	Cytomat2ShakeMode	—	Whether the shaker should be running. Choose Not Supported on a unit with no shaker fitted, and the setting is then ignored.

Set Stack1 Frequency

Sets the frequency of stack 1.

Parameter	Type	Default	Description
Stack 1 Frequency	int	500	Shaking frequency for stack 1, in rpm. Stack 2 is set separately.

Set Stack2 Frequency

Sets the frequency of stack 2.

Parameter	Type	Default	Description
Stack 2 Frequency	int	500	Shaking frequency for stack 2, in rpm. Stack 1 is set separately.

Set Temperature

Sets the incubator's target temperature in degrees Celsius, to one decimal place. The step completes as soon as the incubator accepts the setpoint; use Get Temperature to see how close the chamber has got to it.

Parameter	Type	Default	Description
Temperature	double	—	Target temperature in degrees Celsius. The value is sent to the incubator to one decimal place.

Show Extended Options Settings

Reads the option settings the unit reports for itself and shows them in the Revolution console. Only the transfer station options are decoded, covering which variants are fitted and which position each sits on, and these are configuration flags rather than the live status shown by Show Status.

Show Extended Status

Reads the unit's extended status register and shows it in the Revolution console: separate busy flags for the external, upper and lower systems, the upper and lower gate positions, the device door, and which transfer stations are occupied. Not every unit answers this request, and on one that does not the step fails with a comms error instead of reporting a status.

Show Status

Reads the unit's status register and shows it in the Revolution console: the busy, ready, warning and error flags, whether the handler and the transfer station are occupied, and whether the automatic lift door and the device door are open. Nothing moves and no stored record is changed.

Start Self Scan

Re-scans the store locations in the given range and corrects the storage manager's record for just those positions, recording as empty any location where no barcode can be read. Only one scan can run on a unit at a time, and the step waits for the whole range to be scanned before it completes.

Parameter	Type	Default	Description
First Store Location	int	—	The first store location the scan covers. Locations below it are left alone, so the storage manager keeps whatever it already records for them.
Last Store Location	int	—	The last store location the scan covers. Both ends of the range are included, so setting this to the same value as the first location re-scans a single location.

Start Self Scan Full

Re-scans every location in this unit's layout and rebuilds the storage manager's record of it from the barcodes read, recording as empty any location where no barcode can be read. On a large store this can take more than thirty minutes, and the step waits for the whole scan to finish.

Turn Shake Off

Stops the shaker and leaves it stopped, so it is not restarted the next time a plate is stored or retrieved. The step waits for the incubator to confirm that shaking has stopped.

Turn Shake On

Starts the shaker and keeps it running: shaking is stopped automatically while a plate is stored or retrieved, then restarted once the move is done. If the shaker will not start it is initialised and retried up to three times, and the operator is warned if it still fails.