[ome-users] Support for .FLI files from Capture software (HiCAM FLUO high-speed camera)

[Ponti Aaron]

Hello,

we have .FLI files from Lambert Instruments' Capture software (version 1.0.4.0) for the high-speed camera HiCAM FLUO. Images are streamed at high speed and stored as UINT12 (2 pixels in 3 bytes) or optionally as UINT8. The FLIM reader in bio-formats (https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/LiFlimReader.java) does not seem to support 12-bit intensities. Also, when asking bio-formats to return the metadata, the whole file is returned (which suggests that the metadata of standard FLIM .FLI files is organized -- or terminated -- differently).

The file is binary with the first bytes containing metadata information in readable text format. One field is 'hasDarkImage'. If hasDarkImage == 1, the very last frame is a dark image that is subtracted on-the-fly in the software when displaying the frames (but the images are stored raw in the file). The 'exposureTime' is in micro seconds. Finally, the software seems to support 'compression', although there is no setting for turning it on in the software. The software supports binning.

Would you be interested in adding support for these files to bio-formats? We have example files that we could upload.

Thanks a lot,
a2

----
Dr. Aaron Ponti
Software and Data Management Engineer
Image Analysis Specialist
Single Cell Facility
Department of Biosystems Science and Engineering (D-BSSE)
ETH Zürich
Office 2.30
Mattenstrasse 26
4058 Basel, Switzerland
aaron.ponti at bsse.ethz.ch<mailto:aaron.ponti at bsse.ethz.ch>
T: +41 61 387 33 74
F: +41 61 387 39 93

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