pudu.calibration

Classes for automated plate-reader calibration following the iGEM 2022 InterLab calibration protocol.

Two protocols are provided:

  • GFPODCalibration — two calibrants (fluorescein and silica microspheres), two replicates each; for GFP fluorescence and OD600 calibration.

  • RGBODCalibration — four calibrants (fluorescein, sulforhodamine 101, cascade blue, microspheres), two replicates each; for RGB fluorescence and OD600 calibration.

Both subclass BaseCalibration and use the template-method pattern: run() is implemented in the base class and calls abstract methods for the calibrant-specific steps.

Reference protocol: iGEM 2022 InterLab Calibration Protocol

class pudu.calibration.BaseCalibration(aspiration_rate=0.5, dispense_rate=1.0, tiprack_labware='opentrons_96_tiprack_300ul', tiprack_position='9', pipette='p300_single_gen2', pipette_position='left', calibration_plate_labware='corning_96_wellplate_360ul_flat', calibration_plate_position='7', tube_rack_labware='opentrons_24_aluminumblock_nest_1.5ml_snapcap', tube_rack_position='1', use_falcon_tubes=False, falcon_tube_rack_labware='opentrons_6_tuberack_falcon_50ml_conical', falcon_tube_rack_position='2', take_picture=False, take_video=False, water_testing=False)[source]

Bases: ABC

Abstract base class for calibration protocols. Contains shared hardware setup, liquid handling, and serial dilution functionality. Reference: iGEM 2022 InterLab Calibration Protocol

Parameters:

  • aspiration_rate (float)

  • dispense_rate (float)

  • tiprack_labware (str)

  • tiprack_position (str)

  • pipette (str)

  • pipette_position (str)

  • calibration_plate_labware (str)

  • calibration_plate_position (str)

  • tube_rack_labware (str)

  • tube_rack_position (str)

  • use_falcon_tubes (bool)

  • falcon_tube_rack_labware (str)

  • falcon_tube_rack_position (str)

  • take_picture (bool)

  • take_video (bool)

  • water_testing (bool)

__init__(aspiration_rate=0.5, dispense_rate=1.0, tiprack_labware='opentrons_96_tiprack_300ul', tiprack_position='9', pipette='p300_single_gen2', pipette_position='left', calibration_plate_labware='corning_96_wellplate_360ul_flat', calibration_plate_position='7', tube_rack_labware='opentrons_24_aluminumblock_nest_1.5ml_snapcap', tube_rack_position='1', use_falcon_tubes=False, falcon_tube_rack_labware='opentrons_6_tuberack_falcon_50ml_conical', falcon_tube_rack_position='2', take_picture=False, take_video=False, water_testing=False)[source]

Initialize shared calibration protocol parameters.

Parameters:

  • aspiration_rate (float) – Aspiration speed as a fraction of the pipette’s maximum flow rate (1.0 = full speed). Lower values reduce bubble formation with viscous calibrants.

  • dispense_rate (float) – Dispense speed as a fraction of the pipette’s maximum flow rate.

  • tiprack_labware (str) – Opentrons labware definition string for the tip rack.

  • tiprack_position (str) – Deck slot string for the tip rack.

  • pipette (str) – Opentrons pipette model string (e.g. 'p300_single_gen2').

  • pipette_position (str) – Mount side for the pipette ('left' or 'right').

  • calibration_plate_labware (str) – Opentrons labware definition string for the 96-well calibration plate where serial dilutions are performed.

  • calibration_plate_position (str) – Deck slot string for the calibration plate.

  • tube_rack_labware (str) – Opentrons labware definition string for the 24-well aluminum block / tube rack holding calibrant stocks and buffers.

  • tube_rack_position (str) – Deck slot string for the tube rack.

  • use_falcon_tubes (bool) – If True, PBS and water buffers are sourced from 50 mL Falcon tubes instead of 1.5 mL microtubes. Enables the SmartPipette conical-tube height calculation for accurate aspiration as the tube empties.

  • falcon_tube_rack_labware (str) – Opentrons labware definition string for the Falcon tube rack. Only used when use_falcon_tubes=True.

  • falcon_tube_rack_position (str) – Deck slot string for the Falcon tube rack.

  • take_picture (bool) – If True, capture an image at the start and end of the protocol.

  • take_video (bool) – If True, record video for the duration of the protocol.

  • water_testing (bool) – If True, skip any steps that require real reagents (reserved for future dry-run support; not fully implemented in all subclasses).

run(protocol)[source]

Main protocol execution using template method pattern

Parameters:

protocol (ProtocolContext)

class pudu.calibration.GFPODCalibration(aspiration_rate=0.5, dispense_rate=1.0, tiprack_labware='opentrons_96_tiprack_300ul', tiprack_position='9', pipette='p300_single_gen2', pipette_position='left', calibration_plate_labware='corning_96_wellplate_360ul_flat', calibration_plate_position='7', tube_rack_labware='opentrons_24_aluminumblock_nest_1.5ml_snapcap', tube_rack_position='1', use_falcon_tubes=False, falcon_tube_rack_labware='opentrons_6_tuberack_falcon_50ml_conical', falcon_tube_rack_position='2', take_picture=False, take_video=False, water_testing=False)[source]

Bases: BaseCalibration

GFP and OD600 calibration using fluorescein and nanoparticles. Based on iGEM 2022 calibration protocol.

Parameters:

  • aspiration_rate (float)

  • dispense_rate (float)

  • tiprack_labware (str)

  • tiprack_position (str)

  • pipette (str)

  • pipette_position (str)

  • calibration_plate_labware (str)

  • calibration_plate_position (str)

  • tube_rack_labware (str)

  • tube_rack_position (str)

  • use_falcon_tubes (bool)

  • falcon_tube_rack_labware (str)

  • falcon_tube_rack_position (str)

  • take_picture (bool)

  • take_video (bool)

  • water_testing (bool)

class pudu.calibration.RGBODCalibration(aspiration_rate=0.5, dispense_rate=1.0, tiprack_labware='opentrons_96_tiprack_300ul', tiprack_position='9', pipette='p300_single_gen2', pipette_position='left', calibration_plate_labware='corning_96_wellplate_360ul_flat', calibration_plate_position='7', tube_rack_labware='opentrons_24_aluminumblock_nest_1.5ml_snapcap', tube_rack_position='1', use_falcon_tubes=False, falcon_tube_rack_labware='opentrons_6_tuberack_falcon_50ml_conical', falcon_tube_rack_position='2', take_picture=False, take_video=False, water_testing=False)[source]

Bases: BaseCalibration

RGB and OD600 calibration using fluorescein, sulforhodamine 101, cascade blue, and nanoparticles. Extended iGEM calibration protocol.

Parameters:

  • aspiration_rate (float)

  • dispense_rate (float)

  • tiprack_labware (str)

  • tiprack_position (str)

  • pipette (str)

  • pipette_position (str)

  • calibration_plate_labware (str)

  • calibration_plate_position (str)

  • tube_rack_labware (str)

  • tube_rack_position (str)

  • use_falcon_tubes (bool)

  • falcon_tube_rack_labware (str)

  • falcon_tube_rack_position (str)

  • take_picture (bool)

  • take_video (bool)

  • water_testing (bool)