tritemio
commented
9 years ago On second thought, I prefer the following layout. The concept does not change but in this manner, we can share "logic" between the different measurement types:
/photon_data
timestamps
detectors
...
measurement_specs/
measurement_type: "smFRET", "smFRET-usALEX", etc...
detectors_specs/
# For all 2-color detection measurements
donor
acceptor
# For all 3-color detection measurements
blue
green
red
# For measurements that record polarization
polarization1
polarization2
# For us-ALEX, 2, 3 or N colors
alex_period
# For ns-ALEX (or lifetime with no alternation, i.e. simulations)
laser_pulse_rate
# For 2-color us-ALEX and ns-ALEX (optional)
alex_period_donor
alex_period_acceptor
# For 3-color us-ALEX and ns-ALEX (optional)
alex_period_blue
alex_period_green
alex_period_red[X: What happens when you have spectral and polarization information?]
talaurence
smXplorer
This document summarizes the new layout proposed for version 0.3 of the Photon-HDF5 file format.
The format includes a mandatory set of root fields, and at least a photon-data group.
Root group
Measurement description fields
The following parameters in the root group are present in all types of measurement. They are sufficiently general to warrant their inclusion in all files. Measurement-specific information necessary to interpret the data, is provided in measurement-specific group(s) described later.
/num_spotsnumber of parallel excitation and/or detection spots. When using point-like detectors, this number indicates the number of detection PSFs, even if the excitation does not involves "spots".With a widefield detector this field looses any meaning and its value should become 'undefined', or the field should be removed altogether.
/alex(boolean) True (i.e. = 1) when the measurements uses any form of alternated/interleaved excitation at different wavelengths (us-ALEX, ns-ALEX or PIE, PAX). When there is no periodic alternation of the excitation wavelength this field must beFalse./lifetime(boolean) True (i.e. = 1) when the data contains explicitly a nanotime array. In the case of high-resolution timestamps with potential lifetime resolving resolution this filed will still beFalse./num_spectral_ch(integer) number of different spectral bands in the detection channels (e.g. 2 for 2-color smFRET)/num_polariz_ch(integer) number of different polarizations in the detection channels. The value is 1 if no polarization selection is performed and 2 if two polarizations are recorded./acquisition_timemeasurement duration [X: define. Is it the difference between the last and first timestamp or some different measure?]/measurement_description(string): free-form user-supplied description of the measurement.Note 1: to be decided if all these parameters must be considered mandatory.
Note 2: having these root parameters allows to support "incomplete" or "test" measurements that are not smFRET, and or ALEX. For example the multi-spot preliminary measurements with one laser excitation and one detection band. These simple "test" measurements don't need to have a separate measurement group because these root parameters are enough for interpretation. In other words we keep the simple case simple.
Measurement type
The field:
contains a string that identifies the measurement type. Examples of possible values are:
Measurement group:
This group named
measurements_specsis placed inside thephoton_datagroup so the multispot case is easily supported."smFRET"
"smFRET us-ALEX"
"smFRET ns-ALEX"
"smFRET us-ALEX-3C"
[X: Not sure BGR is the name you want to give to them. Maybe wavelength_n, n = 1, 2, 3?]
photon-data group layout:
Notes
detectorscan be a 1D array or a 2D array. Each row always represents the detector(s) of one timestamp (represented by a single ID or a n-tuple of ID).detectors_specsgroup is now inmeasurement_specsand defines the associations between detectors and spectral bands or polarization bands.