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.