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photon-hdf5_fields.json
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/
photon-hdf5_fields.json
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{
"/":
"Photon-HDF5: A container for photon data.",
"/acquisition_time":
"Measurement duration in seconds.",
"/comment":
"A user defined comment for the data file.",
"/photon_data":
"Group containing arrays of photon-data (one element per photon).",
"/photon_data/timestamps":
"Array of photon timestamps.",
"/photon_data/detectors":
"Array of detector IDs for each timestamp.",
"/photon_data/nanotimes":
"TCSPC photon arrival time (nanotimes).",
"/photon_data/particles":
"Particle IDs (integer) for each timestamp.",
"/photon_data/timestamps_specs":
"Specifications for timestamps.",
"/photon_data/timestamps_specs/timestamps_unit":
"Time in seconds of 1-unit increment in timestamps.",
"/photon_data/nanotimes_specs":
"Group for nanotime-specific data.",
"/photon_data/nanotimes_specs/tcspc_unit":
"TCSPC time bin duration in seconds (nanotimes unit).",
"/photon_data/nanotimes_specs/tcspc_num_bins":
"Number of TCSPC bins.",
"/photon_data/nanotimes_specs/tcspc_range":
"TCSPC full-scale range in seconds.",
"/photon_data/nanotimes_specs/time_reversed":
"True (i.e. 1) if nanotimes contains the time elapsed between a photon and the next laser pulse. False (i.e. 0) if it contains the time elapsed between a laser pulse and a photon.",
"/photon_data/measurement_specs":
"Metadata necessary for interpretation of the particular type of measurement.",
"/photon_data/measurement_specs/measurement_type":
"Name of the measurement the data represents.",
"/photon_data/measurement_specs/alex_period":
"Period of laser alternation in us-ALEX measurements in timestamps units.",
"/photon_data/measurement_specs/laser_pulse_rate":
"Repetition rate of the pulsed excitation laser.",
"/photon_data/measurement_specs/alex_period_excitation1":
"Values pair (start-stop range) identifying photons in the excitation period of wavelength 1 (the shortest).",
"/photon_data/measurement_specs/alex_period_excitation2":
"Values pair (start-stop range) identifying photons in the excitation period of wavelength 2.",
"/photon_data/measurement_specs/detectors_specs":
"Mapping between the detector IDs and the detection channels.",
"/photon_data/measurement_specs/detectors_specs/spectral_ch1":
"Pixel IDs for the first spectral channel (i.e. donor in a 2-color smFRET measurement).",
"/photon_data/measurement_specs/detectors_specs/spectral_ch2":
"Pixel IDs for the first spectral channel (i.e. acceptor in a 2-color smFRET measurement).",
"/photon_data/measurement_specs/detectors_specs/polarization_ch1":
"Pixel IDs for the first polarization channel.",
"/photon_data/measurement_specs/detectors_specs/polarization_ch2":
"Pixel IDs for the second polarization channel.",
"/photon_data/measurement_specs/detectors_specs/split_ch1":
"Pixel IDs for the first channel split through a non-polarizing beam splitter.",
"/photon_data/measurement_specs/detectors_specs/split_ch2":
"Pixel IDs for the second channel split through a non-polarizing beam splitter.",
"/photon_data/measurement_specs/detectors_specs/labels":
"User defined labels for each pixel IDs. In smFRET it is strongly suggested to use \"donor\" and \"acceptor\" for the respective pixel IDs.",
"/setup":
"Information about the experimental setup.",
"/setup/num_pixels":
"Total number of detector pixels.",
"/setup/num_spots":
"Number of excitation (or detection) \"spots\" in the sample.",
"/setup/num_spectral_ch":
"Number of distinct spectral bands that are acquired.",
"/setup/num_polarization_ch":
"Number of distinct polarization states that are acquired.",
"/setup/num_split_ch":
"Number of distinct detection channels detecting the same spectral band and polarization. These are channels are > 1 when using a non-polarizing beam splitter.",
"/setup/modulated_excitation":
"True (or 1) if there is any form of excitation modulation either in the wavelength space (as in us-ALEX or PAX) or in the polarization space. This field is also True for pulse-interleaved excitation (PIE) or ns-ALEX measurements.",
"/setup/lifetime":
"True (or 1) if the measurements includes a nanotimes array of (usually sub-ns resolution) photon arrival times with respect to a laser pulse (as in TCSPC measurements).",
"/setup/excitation_wavelengths":
"List of excitation wavelengths (center wavelength if broad-band) in increasing order (unit: meter).",
"/setup/excitation_cw":
"For each excitation source, this field indicates whether excitation is continuous wave (CW), True (i.e. 1), or pulsed, False (i.e. 0).",
"/setup/excitation_polarizations":
"List of polarization angles (in degrees) for each excitation source.",
"/setup/excitation_input_powers":
"Excitation power in Watts for each excitation source. This is the excitation power entering the optical system.",
"/setup/excitation_intensity":
"Excitation intensity in the sample for each excitation source (units: Watts/meters^2). In the case of confocal excitation this is the peak PSF intensity.",
"/setup/detection_wavelengths":
"Reference wavelengths (m) for each detected spectral band.",
"/setup/detection_polarizations":
"Polarization angles for each detected polarization.",
"/setup/detection_split_ch_ratios":
"Power fraction detected by each \"beam-split\" channel (i.e. independent detection channels obtained through a non-polarizing beam splitter).",
"/identity":
"Information about the Photon-HDF5 data file.",
"/identity/author":
"Author of the current data file.",
"/identity/author_affiliation":
"Company or institution the author is affiliated with.",
"/identity/creator":
"Creator of the current Photon-HDF5 file.",
"/identity/creator_affiliation":
"Company or institution the creator is affiliated with.",
"/identity/url":
"URL that allow to download the Photon-HDF5 data file.",
"/identity/doi":
"Digital Object Identifier (DOI) for the Photon-HDF5 data file.",
"/identity/filename":
"Original file name of the current Photon-HDF5 file (i.e. file name at creation time).",
"/identity/filename_full":
"Original file name (with full path) of the current Photon-HDF5 file (i.e. full file name at creation time).",
"/identity/creation_time":
"Creation time of the current Photon-HDF5 file.",
"/identity/software":
"Name of the software used to create the current Photon-HDF5 file.",
"/identity/software_version":
"Version of the software used to create current the Photon-HDF5 file.",
"/identity/format_name":
"Name of the file format.",
"/identity/format_version":
"Version for the Photon-HDF5 format.",
"/identity/format_url":
"Official URL for the Photon-HDF5 format.",
"/provenance":
"Information about the original data file.",
"/provenance/filename":
"File name of the original data file before conversion to Photon-HDF5.",
"/provenance/filename_full":
"File name (with full path) of the original data file before conversion to Photon-HDF5.",
"/provenance/creation_time":
"Creation time of the original data file.",
"/provenance/modification_time":
"Time of last modification of the original data file.",
"/provenance/software":
"Software used to save the original data file.",
"/provenance/software_version":
"Version of the software used to save the original data file.",
"/sample":
"Information about the measured sample.",
"/sample/num_dyes":
"Number of different dyes present in the samples.",
"/sample/dye_names":
"List of dye names present in the sample.",
"/sample/buffer_name":
"A descriptive name for the buffer.",
"/sample/sample_name":
"A descriptive name for the sample."
}