Installing Labware!

This example notebook will show you how to install labware on a machine with a lab automation deck and navigate wells. It assumes you know a little bit about the laboratory automation deck.

Before Starting:

• Clear any existing items off the bed of your machine!

• A lab automation deck should be installed on your machine.

Import modules and connect to the machine

# Import necessary modules
from science_jubilee.Machine import Machine
from science_jubilee.labware.Labware import Labware

# Connect to the machine
m = Machine(address='192.168.1.2')

# m.home_all() # if you need to, uncomment this line to home the machine

Load the Deck configuration

deck = m.load_deck('POSE-calibrated-deck')
deck.slots  # Slots are empty to start

Load Labware

Now we can tell science jubilee what labware we’d like to install! Each labware has an associated definition which specifies how the wells of this labware are laid out. In general, labware is named in the following format:

<brand>_<number_of_wells>_<labware_type>_<well_volume>_<extra_identifiers>.json

For example, a Falcon brand 96 well plate has the name falcon_96_wellplate_360ul_flat.json.

In general there might be slight differences between labware from different brands!

# We can check all the existing labware definitions:
Labware.list_labware_definitions()

As an example, we’ll install a Falcon 96 well plate into slot 0, and a generic petri dish into slot 1. First, we’ll load them in software:

# Specify the slot to install your labware
# Change the name of the labware if you're using something different!
labwareA = m.load_labware("falcon_96_wellplate_360ul_flat", 1)        # (labware name, slot number)
labwareB = m.load_labware("generic_petri_dish_100ml", 1)              # the petri dish wont 'lock in' to the slot

# You can see that Slots 0 and 1 are now populated
deck.slots

The above code loaded the labware digitally; now we need to physically install the labware in the machine!

The following cell will drop the bed down so you have room to install the labware. When installing, be sure to orient the labware correctly: Well A1 should be on the side closer to the rail where the tools are parked:

Remember also to remove any lids from the labware.

# Physically install your labware into the relevant slots of the machine!
# You can drop the bed down to make room for this
# The machine will move when you run this cell!
m.move_to(z = 150)

Safety Considerations

Note that when we directly move around the machine (e.g. with move_to commands), there is nothing stopping us from colliding with installed labware! This is useful if you want to e.g. probe inside a well, but be careful before sending commands with labware installed. Whend doing liquid handling (e.g. with a pipette tool), there are some built-in safety features to avoid this sort of thing.

Navigating Labware

# You can access wells of your labware by ID. For example, to get the x and y position of a well:
well = labwareA["A1"]
print(well.x, well.y) # the x and y coordinates of the well

# Now you can move to that well
m.move_to(z = 150)                  # Conservatively drop the bed down before moving
m.move_to(x = well.x, y = well.y)

# The petri dish only has one well
petri = labwareB["A1"]
print(petri.x, petri.y)

# Now you can move to the petri dish
m.move_to(z = 150)                  # Conservatively drop the bed down before moving
m.move_to(x = petri.x, y = petri.y)