Photosystem II efficiency (ϕₗₗ)

Basic protocol to measure the Photosystem II efficiency called phi2 or \(\Phi_{II}\). From the fluorescence trace several more values are produced, including \(F_{S}\), the steady state fluorescence, \(F_{M}\), the maximum fluorescence, and LEF, the linear electron flow, based on phi2 and the ambient light intensity.

Basic Usage

Example: Import statement for the phi2 protocol

## Import phi2
from jii_multispeq_protocols.protocols import phi2 as _phi2

---

Sequence

        %%{
init: {
  "theme": "base",
  "themeVariables": {"primaryColor": "#49e06d", "primaryTextColor": "#005e5e", "primaryBorderColor": "#005e5e", "lineColor": "#fff381", "secondaryColor": "#afd7f4", "tertiaryColor": "#D7EBF9"}
}
}%%
flowchart LR
     START((Start))
     A0["`**Protocol**
*Detector:* 700nm - 1150nm
*Pulsed LED:* 590nm (Main)
*Non Pulsed LED:* 655nm (Main)
*Sensor:* PAR light sensor`"]:::protocol
     START ==>|"`**Waits until**: Clamp opened and closed`"| A0
     A0 ==> END
     END(( End ))
     classDef protocol text-align:left,white-space:pre;
    

---

Details

Code

Protocol Code

[  {  'detectors': [[1], [1], [1]],
      'environmental': [['light_intensity']],
      'nonpulsed_lights': [[2], [2], [2]],
      'nonpulsed_lights_brightness': [  ['light_intensity'],
                                        [4500],
                                        ['light_intensity']],
      'open_close_start': 1,
      'pulse_distance': [10000, 10000, 10000],
      'pulse_length': [[30], [30], [30]],
      'pulsed_lights': [[3], [3], [3]],
      'pulsed_lights_brightness': [[2000], [2000], [2000]],
      'pulses': [20, 50, 20]}]

---

Analysis

Usage

Analysis Example (requires JII-MultispeQ package)

from jii_multispeq import measurement as _measurement
from jii_multispeq_protocols.protocols import phi2 as _phi2

## Take a measurement using the MultispeQ
data, crc32 = _measurement.measure(port="<Selected Port>", protocol=_phi2, filename=None, notes="")

## The analyze function of JII-MultispeQ helps to provide the correct format
output = _measurement.analyze( data, _phi2._analyze )

## View Analysis output (as table)
_measurement.view( output )

Function Details

_analyze(_data)

Macro for data evaluation on PhotosynQ.org by: John Doe created: June 4, 2018 4:00 PM

Example Data

Parameter	Value
device_battery	100
device_firmware	1.2
device_id	00:00:00:01
device_name	MultispeQ
device_version	1
Fmp	20931.8
Fs	15306.5
LEF	2.170781335097794
PAR	17.95
Phi2	0.26874420737824745

(png, hires.png, pdf)

Figure: Recorded or calculated trace for Fluorescence Trace.