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{
"/": [
"A file format for photon-counting detector based single-molecule spectroscopy experiments.",
"group"
],
"/acquisition_duration": [
"Measurement duration in seconds.",
"scalar"
],
"/description": [
"A user-defined comment describing the data file.",
"string"
],
"/photon_data": [
"Group containing arrays of photon-data.",
"group"
],
"/photon_data/timestamps": [
"Array of photon timestamps. Units specified in timestamps_units (defined in timestamps_specs/).",
"array"
],
"/photon_data/detectors": [
"Array of pixel IDs for each timestamp.",
"array"
],
"/photon_data/nanotimes": [
"TCSPC photon arrival time (nanotimes). Units and other specifications are in nanotimes_specs group.",
"array"
],
"/photon_data/particles": [
"Particle IDs (integer) for each timestamp.",
"array"
],
"/photon_data/timestamps_specs": [
"Specifications for timestamps.",
"group"
],
"/photon_data/timestamps_specs/timestamps_unit": [
"Value of 1-unit timestamp-increment in seconds.",
"scalar"
],
"/photon_data/nanotimes_specs": [
"Group for nanotime-specific data.",
"group"
],
"/photon_data/nanotimes_specs/tcspc_unit": [
"Value of 1-unit nanotime-increment in seconds (TCSPC bin size).",
"scalar"
],
"/photon_data/nanotimes_specs/tcspc_num_bins": [
"Number of TCSPC bins.",
"scalar"
],
"/photon_data/nanotimes_specs/tcspc_range": [
"TCSPC full-scale range in seconds.",
"scalar"
],
"/photon_data/measurement_specs": [
"Metadata necessary for interpretation of the particular type of measurement.",
"group"
],
"/photon_data/measurement_specs/measurement_type": [
"Name of the measurement the data represents.",
"string"
],
"/photon_data/measurement_specs/alex_period": [
"Period of laser alternation in us-ALEX measurements in timestamps units (defined in timestamps_specs/).",
"scalar"
],
"/photon_data/measurement_specs/laser_repetition_rate": [
"Repetition rate of the pulsed excitation laser (in Hertz).",
"scalar"
],
"/photon_data/measurement_specs/alex_offset": [
"Time offset (in timestamps unit) to apply to timestamps to obtain a properly aligned alternation histogram.",
"scalar"
],
"/photon_data/measurement_specs/alex_excitation_period1": [
"Values pair (start-stop range, in timestamps units) identifying photons in the excitation period of wavelength 1 (the shortest).",
"array"
],
"/photon_data/measurement_specs/alex_excitation_period2": [
"Values pair (start-stop range, in timestamps units) identifying photons in the excitation period of wavelength 2.",
"array"
],
"/photon_data/measurement_specs/detectors_specs": [
"Mapping between the pixel IDs and the detection channels.",
"group"
],
"/photon_data/measurement_specs/detectors_specs/spectral_ch1": [
"Pixel IDs for the first spectral channel (i.e. donor in a 2-color smFRET measurement).",
"array"
],
"/photon_data/measurement_specs/detectors_specs/spectral_ch2": [
"Pixel IDs for the second spectral channel (i.e. acceptor in a 2-color smFRET measurement).",
"array"
],
"/photon_data/measurement_specs/detectors_specs/spectral_ch3": [
"Pixel IDs for the third spectral detection channel.",
"array"
],
"/photon_data/measurement_specs/detectors_specs/spectral_ch4": [
"Pixel IDs for the fourth spectral detection channel.",
"array"
],
"/photon_data/measurement_specs/detectors_specs/polarization_ch1": [
"Pixel IDs for the first polarization channel.",
"array"
],
"/photon_data/measurement_specs/detectors_specs/polarization_ch2": [
"Pixel IDs for the second polarization channel.",
"array"
],
"/photon_data/measurement_specs/detectors_specs/split_ch1": [
"Pixel IDs for the first channel split through a non-polarizing beam splitter.",
"array"
],
"/photon_data/measurement_specs/detectors_specs/split_ch2": [
"Pixel IDs for the second channel split through a non-polarizing beam splitter.",
"array"
],
"/setup": [
"Information about the experimental setup.",
"group"
],
"/setup/num_pixels": [
"Total number of detector pixels.",
"scalar"
],
"/setup/num_spots": [
"Number of excitation (or detection) \"spots\" in the sample.",
"scalar"
],
"/setup/num_spectral_ch": [
"Number of distinct spectral bands which are acquired.",
"scalar"
],
"/setup/num_polarization_ch": [
"Number of distinct polarization states which are acquired.",
"scalar"
],
"/setup/num_split_ch": [
"Number of distinct detection channels detecting the same spectral band and polarization. This value is > 1 when using a non-polarizing beam splitter.",
"scalar"
],
"/setup/modulated_excitation": [
"True (i.e. 1) if there is any form of excitation modulation of excitation wavelength (as in us-ALEX or PAX) or polarization. This field is also True for pulse-interleaved excitation (PIE) or ns-ALEX measurements.",
"scalar"
],
"/setup/excitation_alternated": [
"New in version 0.5. Indicates whether each excitation source is alternated (True, or 1) or not alternated (False, or 0).",
"array"
],
"/setup/lifetime": [
"True (i.e. 1) if the measurement includes a nanotimes array of photon arrival times with respect to a laser pulse (as in TCSPC measurements).",
"scalar"
],
"/setup/excitation_wavelengths": [
"List of excitation wavelengths (center wavelength if broad-band) in increasing order (unit: meter).",
"array"
],
"/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).",
"array"
],
"/setup/laser_repetition_rates": [
"Repetition rates in Hz for each laser. CW lasers have a value of 0.",
"array"
],
"/setup/excitation_polarizations": [
"List of polarization angles (in degrees) for each excitation source.",
"array"
],
"/setup/excitation_input_powers": [
"Excitation power in Watts for each excitation source. This is the excitation power entering the optical system.",
"array"
],
"/setup/excitation_intensity": [
"Excitation intensity in the sample for each excitation source (units: Watt/meter^2). In the case of confocal excitation this is the peak PSF intensity.",
"array"
],
"/setup/detection_wavelengths": [
"Reference wavelengths (units: meter) for each detected spectral band.",
"array"
],
"/setup/detection_polarizations": [
"Polarization angles (in degrees) for each detected polarization.",
"array"
],
"/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).",
"array"
],
"/setup/detectors": [
"Metadata relative to each detector's pixel. Each field is an array with size equal to the number of the detectors.",
"group"
],
"/setup/detectors/id": [
"Detector IDs as they appear on /photon_data/detectors.",
"array"
],
"/setup/detectors/id_hardware": [
"Original IDs assigned by the acquisition hardware to each detector.",
"array"
],
"/setup/detectors/label": [
"Labels (strings) describing each detector.",
"array"
],
"/setup/detectors/counts": [
"Total number of counts detected by each detector.",
"array"
],
"/setup/detectors/module": [
"The module's name each pixel belongs to.",
"array"
],
"/setup/detectors/position": [
"2-D array of integers containing the X-Y coordinates of each pixel in the array.",
"array"
],
"/setup/detectors/dcr": [
"Dark counts (cps) for each pixel.",
"array"
],
"/setup/detectors/afterpulsing": [
"Afterpulsing probability for each pixel.",
"array"
],
"/setup/detectors/spot": [
"Spot number for each pixel in the measurement.",
"array"
],
"/setup/detectors/tcspc_units": [
"TCSPC bin size in seconds (i.e. nanotimes units) for each pixel.",
"array"
],
"/setup/detectors/tcspc_num_bins": [
"Number of TCSPC bins for each pixel.",
"array"
],
"/identity": [
"Information about the Photon-HDF5 data file.",
"group"
],
"/identity/author": [
"Author of the current data file.",
"string"
],
"/identity/author_affiliation": [
"Company or institution the author is affiliated with.",
"string"
],
"/identity/creator": [
"Creator of the current Photon-HDF5 file.",
"string"
],
"/identity/creator_affiliation": [
"Company or institution the creator is affiliated with.",
"string"
],
"/identity/url": [
"URL that allow to download the Photon-HDF5 data file.",
"string"
],
"/identity/doi": [
"Digital Object Identifier (DOI) for the Photon-HDF5 data file.",
"string"
],
"/identity/filename": [
"Original file name of the current Photon-HDF5 file (i.e. file name at creation time).",
"string"
],
"/identity/filename_full": [
"Original file name (with full path) of the current Photon-HDF5 file (i.e. full file name at creation time).",
"string"
],
"/identity/creation_time": [
"Creation time of the current Photon-HDF5 file.",
"string"
],
"/identity/software": [
"Name of the software used to create the current Photon-HDF5 file.",
"string"
],
"/identity/software_version": [
"Version of the software used to create current the Photon-HDF5 file.",
"string"
],
"/identity/format_name": [
"Name of the file format.",
"string"
],
"/identity/format_version": [
"Version for the Photon-HDF5 format.",
"string"
],
"/identity/format_url": [
"Official URL for the Photon-HDF5 format.",
"string"
],
"/identity/funding": [
"A description of funding sources and/or grants used to produce the data.",
"string"
],
"/identity/license": [
"The license under which the data is released.",
"string"
],
"/provenance": [
"Information about the original data file.",
"group"
],
"/provenance/filename": [
"File name of the original data file before conversion to Photon-HDF5.",
"string"
],
"/provenance/filename_full": [
"File name (with full path) of the original data file before conversion to Photon-HDF5.",
"string"
],
"/provenance/creation_time": [
"Creation time of the original data file.",
"string"
],
"/provenance/modification_time": [
"Time of last modification of the original data file.",
"string"
],
"/provenance/software": [
"Software used to save the original data file.",
"string"
],
"/provenance/software_version": [
"Version of the software used to save the original data file.",
"string"
],
"/sample": [
"Information about the measured sample.",
"group"
],
"/sample/num_dyes": [
"Number of different dyes present in the samples.",
"scalar"
],
"/sample/dye_names": [
"String containing a comma-separated list of dye or fluorophore names.",
"string"
],
"/sample/buffer_name": [
"A descriptive name for the buffer.",
"string"
],
"/sample/sample_name": [
"A descriptive name for the sample.",
"string"
]
}