From ebb1c526983a97e7430e0ece339f0f2a2f1c854d Mon Sep 17 00:00:00 2001 From: vegano1 Date: Thu, 7 Nov 2024 13:29:22 -0500 Subject: [PATCH] feat(hardware-testing): add plate reader factory QC resources. --- .../labware/hellma_reference_plate/1.json | 1127 +++++++++++++++++ .../protocols/plate_reader_qc_protocol.py | 136 ++ 2 files changed, 1263 insertions(+) create mode 100644 hardware-testing/hardware_testing/labware/hellma_reference_plate/1.json create mode 100644 hardware-testing/hardware_testing/protocols/plate_reader_qc_protocol.py diff --git a/hardware-testing/hardware_testing/labware/hellma_reference_plate/1.json b/hardware-testing/hardware_testing/labware/hellma_reference_plate/1.json new file mode 100644 index 00000000000..3b56adf18bc --- /dev/null +++ b/hardware-testing/hardware_testing/labware/hellma_reference_plate/1.json @@ -0,0 +1,1127 @@ +{ + "ordering": [ + [ + "A1", + "B1", + "C1", + "D1", + "E1", + "F1", + "G1", + "H1" + ], + [ + "A2", + "B2", + "C2", + "D2", + "E2", + "F2", + "G2", + "H2" + ], + [ + "A3", + "B3", + "C3", + "D3", + "E3", + "F3", + "G3", + "H3" + ], + [ + "A4", + "B4", + "C4", + "D4", + "E4", + "F4", + "G4", + "H4" + ], + [ + "A5", + "B5", + "C5", + "D5", + "E5", + "F5", + "G5", + "H5" + ], + [ + "A6", + "B6", + "C6", + "D6", + "E6", + "F6", + "G6", + "H6" + ], + [ + "A7", + "B7", + "C7", + "D7", + "E7", + "F7", + "G7", + "H7" + ], + [ + "A8", + "B8", + "C8", + "D8", + "E8", + "F8", + "G8", + "H8" + ], + [ + "A9", + "B9", + "C9", + "D9", + "E9", + "F9", + "G9", + "H9" + ], + [ + "A10", + "B10", + "C10", + "D10", + "E10", + "F10", + "G10", + "H10" + ], + [ + "A11", + "B11", + "C11", + "D11", + "E11", + "F11", + "G11", + "H11" + ], + [ + "A12", + "B12", + "C12", + "D12", + "E12", + "F12", + "G12", + "H12" + ] + ], + "brand": { + "brand": "Hellma", + "brandId": [ + "666-R013 Reference Plate" + ] + }, + "metadata": { + "displayName": "Hellma Reference Plate", + "displayCategory": "wellPlate", + "displayVolumeUnits": "µL", + "tags": [] + 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] + } + ], + "parameters": { + "format": "irregular", + "quirks": [], + "isTiprack": false, + "isMagneticModuleCompatible": false, + "loadName": "hellma_reference_plate" + }, + "namespace": "custom_beta", + "version": 1, + "schemaVersion": 2, + "cornerOffsetFromSlot": { + "x": 0, + "y": 0, + "z": 0 + } +} diff --git a/hardware-testing/hardware_testing/protocols/plate_reader_qc_protocol.py b/hardware-testing/hardware_testing/protocols/plate_reader_qc_protocol.py new file mode 100644 index 00000000000..a2ed0689bd9 --- /dev/null +++ b/hardware-testing/hardware_testing/protocols/plate_reader_qc_protocol.py @@ -0,0 +1,136 @@ +from opentrons import protocol_api +import numpy as np + +# metadata +metadata = { + 'protocolName': 'Absorbance Plate Reader Reference Plate QA', + 'author': 'QA', +} + +requirements = { + "robotType": "Flex", + "apiLevel": "2.21", +} + + +def convert_read_dictionary_to_array(read_data): + """Convert a dictionary of read results to an array + + Converts a dictionary of OD values, as formatted by the Opentrons API's + plate reader read() function, to a 2D numpy.array of shape (8,12) for + further processing. + + read_data: dict + a dictonary of read values with celll numbers for keys, e.g. 'A1' + """ + data = np.empty((8,12)) + for key, value in read_data.items(): + row_index = ord(key[0]) - ord('A') + column_index = int(key[1:]) - 1 + data[row_index][column_index] = value + + return data + + +def check_plate_reader_accuracy(read_data, flipped=False): + """Check the accuracy of a measurement result returned by the read() method + + data: dictionary of plate reader absorbance valurs + as returned by the absorbanceReaderV1 read() method + flipped: bool + True if reference plate was rotated 180 degrees for measurment + """ + + # These are the hard-coded calibration values for Hellma 666-R013 with Serial + # Number 101934. If you're using a different reference plate you must update + # these values with the ones provided by Hellma with your reference plate + cal_values_450nm = np.array([ + [0. , 0. , 0.245 , 0.245 , 0.4973, 0.4973, 0.9897, 0.9897, 1.5258, 1.5258, 2.537 , 2.537 ], + [0. , 0. , 0.2451, 0.2451, 0.4972, 0.4972, 0.9877, 0.9877, 1.5253, 1.5253, 2.535 , 2.535 ], + [0. , 0. , 0.2451, 0.2451, 0.4973, 0.4973, 0.9871, 0.9871, 1.5246, 1.5246, 2.536 , 2.536 ], + [0. , 0. , 0.2452, 0.2452, 0.4974, 0.4974, 0.9872, 0.9872, 1.525 , 1.525 , 2.535 , 2.535 ], + [0. , 0. , 0.2452, 0.2452, 0.4976, 0.4976, 0.9872, 0.9872, 1.5248, 1.5248, 2.535 , 2.535 ], + [0. , 0. , 0.2454, 0.2454, 0.4977, 0.4977, 0.9874, 0.9874, 1.5245, 1.5245, 2.536 , 2.536 ], + [0. , 0. , 0.2453, 0.2453, 0.4977, 0.4977, 0.9876, 0.9876, 1.5245, 1.5245, 2.533 , 2.533 ], + [0. , 0. , 0.2456, 0.2456, 0.4977, 0.4977, 0.9891, 0.9891, 1.5243, 1.5243, 2.533 , 2.533 ] + ]) + cal_values_650nm = np.array([ + [0. , 0. , 0.2958, 0.2958, 0.5537, 0.5537, 0.9944, 0.9944, 1.4232, 1.4232, 2.372 , 2.372 ], + [0. , 0. , 0.296 , 0.296 , 0.5535, 0.5535, 0.9924, 0.9924, 1.4235, 1.4235, 2.37 , 2.37 ], + [0. , 0. , 0.296 , 0.296 , 0.5534, 0.5534, 0.9919, 0.9919, 1.4228, 1.4228, 2.37 , 2.37 ], + [0. , 0. , 0.2961, 0.2961, 0.5534, 0.5534, 0.9918, 0.9918, 1.423 , 1.423 , 2.369 , 2.369 ], + [0. , 0. , 0.2962, 0.2962, 0.5536, 0.5536, 0.9918, 0.9918, 1.4225, 1.4225, 2.369 , 2.369 ], + [0. , 0. , 0.2964, 0.2964, 0.5535, 0.5535, 0.992 , 0.992 , 1.4223, 1.4223, 2.369 , 2.369 ], + [0. , 0. , 0.2963, 0.2963, 0.5534, 0.5534, 0.9922, 0.9922, 1.4221, 1.4221, 2.368 , 2.368 ], + [0. , 0. , 0.2965, 0.2965, 0.5533, 0.5533, 0.9938, 0.9938, 1.4222, 1.4222, 2.367 , 2.367 ] + ]) + cal_tolerances = np.array( + [0. , 0. , 0.0024, 0.0024, 0.0034, 0.0034, 0.0034, 0.0034, 0.0068, 0.0068, 0.012 , 0.012 ] + ) + + # Calculate absolute accuracy tolerances for each cell + # The last two columns have a higher tolerance per the Byonoy datasheet + # because OD>2.0 and wavelength>=450nm on the Hellma plate + accuracy_tolerances_450nm = np.zeros((8,12)) + accuracy_tolerances_450nm[:,:10] = cal_values_450nm[:,:10]*0.010 + cal_tolerances[:10] + 0.01 + accuracy_tolerances_450nm[:,10:] = cal_values_450nm[:,10:]*0.015 + cal_tolerances[10:] + 0.01 + accuracy_tolerances_650nm = np.zeros((8,12)) + accuracy_tolerances_650nm[:,:10] = cal_values_650nm[:,:10]*0.010 + cal_tolerances[:10] + 0.01 + accuracy_tolerances_650nm[:,10:] = cal_values_650nm[:,10:]*0.015 + cal_tolerances[10:] + 0.01 + + # Convert read result dictionary to numpy array for comparison + data_450nm = convert_read_dictionary_to_array(read_data[450]) + data_650nm = convert_read_dictionary_to_array(read_data[650]) + + # Check accuracy + if (flipped): + within_tolerance_450nm = np.isclose(data_450nm, np.rot90(cal_values_450nm, 2), atol=np.rot90(accuracy_tolerances_450nm, 2)) + within_tolerance_650nm = np.isclose(data_650nm, np.rot90(cal_values_650nm, 2), atol=np.rot90(accuracy_tolerances_650nm, 2)) + else: + within_tolerance_450nm = np.isclose(data_450nm, cal_values_450nm, atol=accuracy_tolerances_450nm) + within_tolerance_650nm = np.isclose(data_650nm, cal_values_650nm, atol=accuracy_tolerances_650nm) + + errors_450nm = np.count_nonzero(np.where(within_tolerance_450nm==False)) + errors_650nm = np.count_nonzero(np.where(within_tolerance_650nm==False)) + msg = f"450nm Failures: {errors_450nm}, 650nm Failures: {errors_650nm}" + + return msg + +# protocol run function +def run(protocol: protocol_api.ProtocolContext): + HELLMA_PLATE_SLOT = "C2" + PLATE_READER_SLOT = "D3" + + plate_reader = protocol.load_module("absorbanceReaderV1", PLATE_READER_SLOT) + hellma_plate = protocol.load_labware("hellma_reference_plate", HELLMA_PLATE_SLOT) + tiprack_1000 = protocol.load_labware(load_name='opentrons_flex_96_tiprack_50ul', location="A2") + trash_labware = protocol.load_trash_bin("A3") + #instrument = protocol.load_instrument("flex_8channel_50", "left", tip_racks=[tiprack_1000]) + instrument = protocol.load_instrument("flex_96channel_1000", "left", tip_racks=[tiprack_1000]) + instrument.trash_container = trash_labware + + # Initialize to multiple wavelengths + plate_reader.initialize('multi', [450, 650]) + + plate_reader.open_lid() + protocol.move_labware(hellma_plate, plate_reader, use_gripper=True) + plate_reader.close_lid() + + # Take reading + result = plate_reader.read() + msg = f"multi: {result}" + protocol.comment(msg=msg) + #protocol.pause(msg=msg) + + # Place the Plate Reader lid back on using the Gripper. + plate_reader.open_lid() + protocol.move_labware(hellma_plate, HELLMA_PLATE_SLOT, use_gripper=True) + plate_reader.close_lid() + + # Check and display accuracy + if result is not None: + #msg = f"multi: {result}" + #msg = f"multi: {result[450]}" + msg = check_plate_reader_accuracy(result, flipped=False) + protocol.comment(msg=msg) + protocol.pause(msg=msg)