Hello World, “Cytomat Incubator”!

The Cytomat series of incubators is used for storing microplates under controlled environmental conditions. PyLabRobot implements the CytomatBackend which supports several models such as C6000, C6002, C2C_50, C2C_425, C2C_450_SHAKE and C5C.

In this tutorial we show how to:

• connect to the incubator

• configure racks

• move plates in and out

• monitor temperature and humidity

Note

This notebook uses await statements which must be run inside an asynchronous environment such as asyncio.

from pylabrobot.incubators import CytomatBackend, CytomatType
from pylabrobot.incubators.cytomat.racks import cytomat_rack_9mm_51
from pylabrobot.incubators.incubator import Incubator
from pylabrobot.resources.corning.plates import Cor_96_wellplate_360ul_Fb
from pylabrobot.resources import Coordinate

# Connect to the incubator via a serial port
backend = CytomatBackend(model=CytomatType.C6000, port="/dev/ttyUSB0")

# Create a rack and assemble an `Incubator` resource
rack = cytomat_rack_9mm_51("rack_A")
incubator = Incubator(
    backend=backend,
    name="cyto",
    size_x=860,
    size_y=550,
    size_z=900,
    racks=[rack],
    loading_tray_location=Coordinate(0, 0, 0),
)

Setup

Setting up the incubator opens the serial connection and initializes the device.

await incubator.setup()

Storing a plate

To store a plate we first place it on the loading tray and then call take_in_plate(). You can choose a site automatically or specify one explicitly.

plate = Cor_96_wellplate_360ul_Fb("my_plate")
incubator.loading_tray.assign_child_resource(plate)
await incubator.take_in_plate("smallest")  # choose the smallest free site

# other options:
# await incubator.take_in_plate("random")  # random free site
# await incubator.take_in_plate(rack[3])  # store at rack position 3

Retrieving a plate

Use fetch_plate_to_loading_tray() to move a plate from storage to the loading tray.

await incubator.fetch_plate_to_loading_tray("my_plate")
retrieved = incubator.loading_tray.resource

Monitoring conditions

The Cytomat provides queries for temperature and humidity.

current_temp = await incubator.get_temperature()
current_humidity = await incubator.backend.get_humidity()
print(current_temp, current_humidity)

Shutdown

Always close the connection when finished.

await incubator.stop()