Protocol Setup

When you start setup for a protocol, you'll see the "Prepare to run" screen, which summarizes all of the requirements for the protocol.

All sections of the "Prepare to run" screen. On the touchscreen, scroll the list to see all sections.

If hardware is not connected or calibrated, you will see a warning icon (exclamation point) and the row will be highlighted in orange. If all requirements are met, you will see a checkmark and the row will be highlighted in green.

Tap any row with a right arrow to show more information for that category. (The one exception is tapping Labware Position Check, which begins that process. See the Labware Position Check section below for more details.)

Category	Description
Instruments	See if all instruments are attached to the correct mounts and calibrated. Tap Attach or Calibrate to set up any that aren't.
Parameters	See the names, descriptions, and default values of runtime parameters for the protocol. Tap a parameter to edit its value. See the Runtime Parameters section below for more details.
Hardware	See the locations and connection statuses of hardware on the deck. Tap Setup Instructions to get detailed instructions. Tap Map View to switch to a visual layout of hardware positions.
Labware	See the locations of labware. Each labware lists its initial deck location, and icons indicate labware that are on top of modules. Tap Map View to switch to a visual layout of labware positions.
Liquids	See the types and total volumes of liquids. Tap any liquid name to expand a list of well-by-well volumes. In turn, tap an individual volume row to show a visual layout of its location within labware.

On any category screen, return to the "Prepare to run" screen by tapping the back arrow in the top left.

Runtime parameters

Runtime parameters customize protocols during setup, letting you adjust pipette types, mount positions, aspirate/dispense volumes, labware types, and more—all without writing a new protocol.

Tap a configurable parameter to modify it. Different types of touchscreen controls are used for different parameter types.

• Boolean: Tap the parameter to toggle its value between On and Off.

• String and numeric choices: Choose from a menu of possible values.

• Numeric range: Use the onscreen keypad to enter a value within the acceptable range.

• CSV: Choose from a file picker.

Using CSV data

Flex looks for CSV files in the root directory of an attached USB drive or files that were used in a previous run of the same protocol. You can connect a USB drive to any open USB port on Flex, but we recommend using the port below the touchscreen. As shown here, this protocol has no CSV files saved on this robot, but there are several on an attached USB drive. Tap the desired CSV file to use its data into your protocol.

When working with CSV files, keep in mind that:

• The touchscreen truncates file names that are longer than 52 characters. You can still upload files with names that exceed the limit.

• The USB drive must use a file system that's readable by the robot. FAT32, NTFS, and ext4 file systems are supported. The HFS+ and APFS file systems are not.

• You must leave the USB drive attached until you start the run, or Flex won't be able to access the CSV data that you chose.

Confirming runtime parameters

Parameter and CSV file selections are still editable until you tap Confirm values. Modifications become read-only after that. To make further adjustments, you'll have to cancel the protocol run and start over.

Labware offsets and position checking

Labware offsets

Labware offsets are fine-tuned positional coordinates that help your robot align its pipette relative to a specific piece of labware. The release of robot software version 8.4 introduced significant improvements to the labware offset and position checking system.

Feature	Description
Protocol independence	Offsets are positional adjustments associated with a piece of labware, rather than with a specific protocol, and saved on the robot. This allows for greater flexibility and reusability of offset data in any protocol.
Default offsets	Default offsets are manually created via Labware Position Check and then automatically applied to each instance of that labware, regardless of deck slot or protocol. This "measure once, set everywhere" feature means you don't have to check offsets for duplicate labware, which helps reduce protocol setup time and effort.
Applied offsets	Applied offsets override defaults for a specific piece of labware in a specific deck slot. You can use an applied offset with different protocols, but the labware and deck slot must be the same as the original applied offset.
Hardcoded offsets	A hardcoded offset is an offset type typically created by advanced users via the Opentrons Python API. Because these offsets are defined in code (set_offset), you cannot change them from the touchscreen or Opentrons App. You’ll need to modify the Python protocol file to change a hardcoded offset. See Setting Labware Offsets.

Offsets at-a-glance

This illustration shows how the different types of offsets appear as you're configuring a protocol on the Flex touchscreen.

Labware Position Check

Labware Position Check lets you align a pipette relative to a piece of labware (e.g., a well plate), which helps ensure accurate and reproducible pipetting results.

You must ensure that each piece of labware used in your protocol has a default or applied offset associated with it. As shown in the example below, you cannot run a protocol (the play button is inactive) if it uses labware that is missing offset data.

Tap Labware Offsets to see which labware is missing an offset and to start Labware Position Check. Refer to the touchscreen or the Opentrons App when running Labware Position Check. It will provide instructions and animations to guide you through this process.

Jog controls

During Labware Position Check, you’ll use the jog controls to align the pipette with the selected labware.

Jog controls used in Labware Position Check.

To use the jog controls:

1. Select a jog control option to set the pipette's axis of movement.
2. Select a jump size to set how far the pipette moves (in mm). You can move the pipette in increments of 0.1, 1, or 10 mm. Use larger jump sizes to move the pipette quickly, but beware of crashing the pipette into labware.
3. Tap an arrow to move the pipette for your selected direction and distance.
4. Tap Close when, in your best judgement, the pipette is optimally aligned with the selected labware.
5. Continue to follow prompts and instructions on the touchscreen to complete the Labware Position Check process.

Note

Labware Position Check corrects for minor, millimeter-scale pipette and labware alignment variations. If you find yourself using it to compensate for large, multi-centimeter offsets, this may suggest an alignment problem related to labware manufacturing defects or incorrect labware definitions. Contact Opentrons Support if you encounter persistent, significant instrument or labware misalignments.