The “generic” measurement type

For measurement types which cannot be described by any other supported measurement_type, it is possible to use the “generic” type and use the /setup fields to describe the exact configuration.

Examples

Below, we list a few examples of measurements described with the “generic” measurement_type.

2-Polarizations

A setup detecting two polarizations in the detection path will be defined by:

/setup/num_spectral_ch = 1
/setup/num_split_ch = 1
/setup/num_polarization_ch = 2

and will also specify the detector used for each polarizations:

/photon_data/measurement_specs/detectors_specs/
    polarization_ch1 = 0
    polarization_ch2 = 1

(where the values 0 and 1 are only examples). In addition /setup/lifetime will indicate whether the measurement has TCSPC data or not. Finally, the optional field /setup/excitation_polarizations can be used to save the angle of each polarization.

2-Split channels

A setup in which the detection (emission) path is split in two using a non-polarizing beam splitter will be defined by:

/setup/num_spectral_ch = 1
/setup/num_split_ch = 2
/setup/num_polarization_ch = 1

and the measurement_specs will contain:

/photon_data/measurement_specs/detectors_specs/
    split_ch1 = 0
    split_ch2 = 1

(where the values 0 and 1 are only examples). In addition /setup/lifetime will indicate whether the measurement has TCSPC data or not. Finally, the optional field /setup/detection_split_ch_ratios can be used to store the “splitting-ratio” of each channel. For example, with a 50-50% beam splitter this field will be [0.5, 0.5].

2-Spectral channels

This case is already covered by the “smFRET” measurement_type both for CW and TCSPC measurements (the two are distinguished with the value of /setup/lifetime).

If a measurement has two spectral detection bands but is fundamentally different from a smFRET measurement, then the “generic” measurement_type can be used. In this case the measurement_specs fields will be the same as in the “smFRET” measurement_type. In particular:

/setup/num_spectral_ch = 2
/setup/num_split_ch = 1
/setup/num_polarization_ch = 1

and:

/photon_data/measurement_specs/detectors_specs/
    spectral_ch1 = 0
    spectral_ch2 = 1

TCSPC measurements

In all previous examples, variants with TCSPC data will be defined by /setup/lifetime = True and the field /photon_data/measurement_specs/laser_repetition_rate specifying the laser repetition rate. When the laser is pulsed but the acquisition hardware is not TCSPC, /setup/excitation_cw will be False and /setup/lifetime = False.

2-Spectral channels + polarization

This is the case of a smFRET measurement where the donor and acceptor emission paths are further split into parallel and perpendicular polarization. In this case, we have:

/setup/num_spectral_ch = 2
/setup/num_split_ch = 1
/setup/num_polarization_ch = 2

Assuming that detectors 0, 1 are used for the two polarizations in the donor channel and detectors 2, 3 for the acceptor channel, we have:

/photon_data/measurement_specs/detectors_specs/
    spectral_ch1 = [0, 1]
    spectral_ch2 = [2, 3]
    polarization_ch1 = [0, 2]
    polarization_ch2 = [1, 3]

ALEX + polarization

In this measurement, μs-ALEX excitation and four detectors are used for the two polarizations in the donor and acceptor paths. This is identical to the previous example, with the difference that there are now two CW alternating lasers.

In this case, we have:

/setup/num_spectral_ch = 2
/setup/num_split_ch = 1
/setup/num_polarization_ch = 2
/setup/excitation_alternated = [True, True]

and, using the detector numbers of the previous example:

/photon_data/measurement_specs/
    alex_period = 4000
    detectors_specs/
        spectral_ch1 = [0, 1]
        spectral_ch2 = [2, 3]
        polarization_ch1 = [0, 2]
        polarization_ch2 = [1, 3]

Note that when /setup/excitation_alternated is True then /photon_data/measurement_specs/alex_period needs to be present.

Notes on “generic” measurement_type

Here we collect a few notes on using the “generic” measurement_type.

When at least one laser is CW and alternated (/setup/excitation_cw and /setup/excitation_alternated), then the photon_data/measurement_specs/alex_period is mandatory.

When at least one laser is pulsed (i.e. False in /setup/excitation_cw), then the fields photon_data/measurement_specs/laser_repetition_rate and /setup/laser_repetition_rates are mandatory.

When /setup/lifetime = True, then the file will have /setup/laser_repetition_rates and photon_data/measurement_specs/laser_repetition_rate.

If there is only one detector per spot photon_data/detectors array may be omitted. In this case, the lack of photon_data/detectors implies no photon_data/measurement_specs/detectors_specs group.