5. Defining new measurement types

If you need to save a type of measurement not included in the list of currently supported measurement types, you need to define a new “measurement_specs”, i.e. which info to put in the measurement_specs group in order to make the dataset self-contained.

5.1. What to put in measurement_specs

First and foremost, a new measurement_specs needs to have a name, i.e. the name associated with the type of measurement to be saved. The name of the measurement-type is a string stored in measurement_specs/measurement_type. This string is used to differentiate between different measurement_specs. For example, names of already defined measurment types are: smFRET, smFRET-usALEX, smFRET-usALEX-3c and smFRET-nsALEX (see here).

Beyond the name, measurement_specs group should contain all the metadata needed to for unambiguous analysis of the dataset. For example, in smFRET experiments the measurement_specs contains the IDs of donor and acceptor detection channels. In Alternated Excitation (ALEX) measurements it will also contains definition of laser alternation (period, range for donor and acceptor, etc...).

In most cases, measurement_specs will contain the association between detector IDs physical detection channels (Detectors specs). Detection channels may differ in the detected spectral band and in detected polarization, called spectral_chX and polarization_chX (where X is 1, 2, ...). When using a non-polarizing beam splitter and both spectral band and polarization are equal, the detection channels are names split_chX (see Beam-split channels).

If possible, new measurement_specs should follow naming conventions of other official measurement_specs.

For any question please use the Photon-HDF5 Google Group.

5.2. How to propose a new measurement_specs

Logistically, the process works as follows.

  1. Users propose new measurement_specs using the Photon-HDF5 Google Group.
  2. After discussion, the measurement_specs will be advertised on the Photon-HDF5 website in order to gather opinions from different parties.
  3. Discussion continues and modifications are proposed until consensus is reached.
  4. Finally, the new measurement_specs becomes official part of Photon-HDF5: it is added to the Photon-HDF5 documentation and software support is added to phconvert.

For any question please use the Photon-HDF5 Google Group.