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FLIMfit Supported File Formats

Supported formats in OMERO

Time-resolved Fluorescence Lifetime data involves a second time dimension (t) in addition to the real-time dimension (T) provided by the standard 5D OME model. The addition of extra dimensions is supported by OMERO as described in

The FLIMfit software will work with any images or images that have been imported into OMERO with the ModuloAlong annotation described and the attribute "Type" set to "lifetime".

For backwards compatibility, the FLIMfit software will also work with two types of Time Correlated Single Photon Counting (TCSPC) data that have been imported into OMERO without this ModuloAlong annotation:

  1. images imported from Becker and Hickl .sdt files.
  2. any image where the extra t dimension is encoded in Z and PhysicalSizeZ is set to the spacing between time-bins. (For compatibility with data imported from LaVision BioTec ImSpector systems by first converting to an OME-TIFF file.)

Points to note

The ModuloAlong annotation described above allows FLIM data to be encoded in any of three dimensions (ZCT). However, we strongly believe that a number of issues of future compatibility with other modalities can be avoided by standardising on the use of one dimension for FLIM.

We therefore intend to use only ModuloAlongT for FLIM data and we would ask other developers to do the same. Thus leaving ModuloAlong Z and C free for other modalities.

Supported file formats

The FLIMfit software can also be used with FLIM data files (rather than via OMERO).

The following file formats are supported:

  1. Becker and Hickl .sdt files
  2. LaVision BioTech .msr files
  3. PicoQuant .bin files (version 4.10+ also support PicoQuant FIFO .ptu and .pt3 files)
  4. OME-TIFF files where a ModuloAlong annotation, as described above, is included and the attribute 'Type' is set to "lifetime"
  5. OME-TIFF files where the extra t dimension is encoded in Z and PhysicalSizeZ is set to the spacing between time-bins (as generated by LaVision BioTec ImSpector systems)
  6. Data where each plane along the t dimension is stored as a separate file and the spacing is encoded in the file name (for use with gated, wide-field FLIM)
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