Fluorescence - Detector Offsets =============================== .. automodule:: jii_multispeq_protocols.protocols.calibrations.fluorescence_detector_offsets_calibration :members: :undoc-members: :show-inheritance: :no-index: :no-title: Basic Usage ----------- .. code-block:: python :caption: *Example:* Import statement for the **fluorescence_detector_offsets_calibration** protocol ## Import fluorescence_detector_offsets_calibration from jii_multispeq_protocols.protocols.calibrations import fluorescence_detector_offsets_calibration as _fluorescence_detector_offsets_calibration ---- Sequence -------- .. mermaid:: %%{ init: { "theme": "base", "themeVariables": {"primaryColor": "#49e06d", "primaryTextColor": "#005e5e", "primaryBorderColor": "#005e5e", "lineColor": "#fff381", "secondaryColor": "#afd7f4", "tertiaryColor": "#D7EBF9"} } }%% flowchart TD START((Start)) A0["`**Protocol** Runs only during *first* repeat`"]:::protocol START ==> A0 A1["`**bc1** *Detector:* • 700nm - 1150nm • 400nm - 700nm (BG18) *Pulsed LEDs:* • 530nm (Main) • 590nm (Main) • 950nm (Clamp) • 820nm (Clamp) *Non Pulsed LED:* `"]:::protocol A0 ==>|"`**Illumination** 655nm (Main) *Duration (ms)*: 0 *PAR*: 200`"| A1 A2["`**bc0** *Detector:* • 700nm - 1150nm • 400nm - 700nm (BG18) *Pulsed LEDs:* • 530nm (Main) • 590nm (Main) • 950nm (Clamp) • 820nm (Clamp) *Non Pulsed LED:* `"]:::protocol A1 ==>|"`**Illumination** 655nm (Main) *Duration (ms)*: 0 *PAR*: 200`"| A2 A2 ==> END A2 -.-> |2x| A0 linkStyle 4 stroke-width:3px END(( End )) classDef protocol text-align:left,white-space:pre; ---- Details ------- Code ~~~~ .. code-block:: python :caption: Protocol Code [ { '_protocol_set_': [ { 'alert': 'Clamp the Fluorescent Card (pink)', 'autogain': [ [1, 1, 3, 15, 50000], [6, 6, 1, 15, 50000], [0, 10, 1, 15, 50000]], 'do_once': 1}, { 'bleed_correction': 1, 'detectors': [ [3, 1, 1, 1], [3, 1, 1, 1], [3, 1, 1, 1]], 'label': 'bc1', 'nonpulsed_lights': [['@s2'], ['@s2'], ['@s2']], 'nonpulsed_lights_brightness': [ [0], ['@p0'], [0]], 'pre_illumination': [2, 0, '@n1:0'], 'protocol_averages': 1, 'protocol_repeats': '#l0', 'pulse_distance': [2000, 2000, 2000], 'pulse_length': [ ['a_d1', 'a_d6', 'a_d0', 20], ['a_d1', 'a_d6', 'a_d0', 20], ['a_d1', 'a_d6', 'a_d0', 20]], 'pulsed_lights': [ [1, 6, 10, 3], [1, 6, 10, 3], [1, 6, 10, 3]], 'pulsed_lights_brightness': [ [ 'a_b1', 'a_b6', 'a_b0', 400], [ 'a_b1', 'a_b6', 'a_b0', 400], [ 'a_b1', 'a_b6', 'a_b0', 400]], 'pulses': ['@n1:1', '@n1:1', '@n1:1'], 'pulses_delay': [1, 1, 1]}, { 'bleed_correction': 0, 'detectors': [ [3, 1, 1, 1], [3, 1, 1, 1], [3, 1, 1, 1]], 'label': 'bc0', 'nonpulsed_lights': [['@s2'], ['@s2'], ['@s2']], 'nonpulsed_lights_brightness': [ [0], ['@p0'], [0]], 'pre_illumination': [2, 0, '@n1:0'], 'protocol_averages': 1, 'protocol_repeats': '#l0', 'pulse_distance': [2000, 2000, 2000], 'pulse_length': [ ['a_d1', 'a_d6', 'a_d0', 20], ['a_d1', 'a_d6', 'a_d0', 20], ['a_d1', 'a_d6', 'a_d0', 20]], 'pulsed_lights': [ [1, 6, 10, 3], [1, 6, 10, 3], [1, 6, 10, 3]], 'pulsed_lights_brightness': [ [ 'a_b1', 'a_b6', 'a_b0', 400], [ 'a_b1', 'a_b6', 'a_b0', 400], [ 'a_b1', 'a_b6', 'a_b0', 400]], 'pulses': ['@n1:1', '@n1:1', '@n1:1'], 'pulses_delay': [1, 1, 1]}], 'set_repeats': '#l2', 'v_arrays': [ [0, -200, -400, -750, -1000, -2000, -3000, -4000], [200, 30], [2, 9], [1, 0, 1, 0]]}] ---- Analysis -------- Usage ~~~~~ .. code-block:: python :caption: Analysis Example (requires ``JII-MultispeQ`` package) from jii_multispeq import measurement as _measurement from jii_multispeq_protocols.protocols.calibrations import fluorescence_detector_offsets_calibration as _fluorescence_detector_offsets_calibration ## Take a measurement using the MultispeQ data, crc32 = _measurement.measure(port="", protocol=_fluorescence_detector_offsets_calibration, filename=None, notes="") ## The analyze function of JII-MultispeQ helps to provide the correct format output = _measurement.analyze( data, _fluorescence_detector_offsets_calibration._analyze ) ## View Analysis output (as table) _measurement.view( output ) Function Details ~~~~~~~~~~~~~~~~ .. autofunction:: jii_multispeq_protocols.protocols.calibrations.fluorescence_detector_offsets_calibration._analyze :no-index: Example Data ~~~~~~~~~~~~ =============== ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= Parameter Value =============== ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= device_battery 98 device_firmware 2.343 device_id 52:00:12:bc device_name MultispeQ device_version 2 status Test OK toDevice bleed3+0+0+0+0+0+0+0+0+0+bleed3+1+0+0+0+0+0+0+0+0+bleed3+2+0+0+0+0+0+0+0+0+bleed3+3+0+0+0+0+0+0+0+0+bleed3+4+0+0+0+0+0+0+0+0+bleed3+5+0+0+0+0+0+0+0+0+bleed3+6+0+0+0+0+0+0+0+0+bleed3+7+0+0+0+0+0+0+0+0+bleed3+8+0+0+0+0+0+0+0+0+bleed3+9+0+0+0+0+0+0+0+0+bleed3+10+0+0+0+0+0+0+0+0+bleed3+11+0+0+0+0+0+0+0+0+bleed3+12+0+0+0+0+0+0+0+0+bleed3+13+0+0+0+0+0+0+0+0+bleed3+14+0+0+0+0+0+0+0+0+bleed3+1+-36.0+201.0+272.0+359.0+418.0+483.0+638.0+745.0+bleed3+3+-6.0+4.0+16.0+28.0+38.0+68.0+116.0+181.0+bleed3+7+-38.0+24.0+5.0+3.0+32.0+62.0+42.0+90.0+bleed3+2+0.0+2.0+1.0+-5.0+-16.0+-27.0+-47.0+-57.0+bleed3+14+-18.0+69.0+182.0+268.0+309.0+548.0+782.0+926.0+bleed3+10+-4.0+94.0+398.0+991.0+1402.0+3018.0+4581.0+6064.0+bleed3+13+-19.0+8.0+41.0+128.0+183.0+452.0+644.0+820.0+bleed3+8+1.0+4.0+10.0+0.0+12.0+19.0+32.0+47.0+setCalTime+2+setCalOK+2+0+ =============== =============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================