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

[Johan Herz]

Hello Sebastien,

Thank you for your reply.

I have 2 files, 6 GB each.
They are made with 2 different versions of Capture our Hi-speed recording
software.
We make use of the .fli format and we tried to be as compatible with the
Bio-formats as possible.
Unfortunately, we could not work around the 12 bit, hence the unsupported
data format.

Personally, I have tried to get bio-formats to compile on my one machine, I
made a checkout, but I ran in too many problems. It seems that you are
planning to have a new release.
Because I wanted to fix the problem of not being able to open files having
a filesize bigger than 2 GB.

So could you take this in to account as well? To open our files
virtual, FiJi supports this, right?

Is it okay for you if I share the files through Google Drive, as they are
too big to upload to your server?


 Recording_Capture_1.1.fli
<https://drive.google.com/a/lambertinstruments.com/file/d/1xw43lsucOssXb97ia0JJCCZ9467hV3iO/view?usp=drive_web>

 Recording_Capture_1.0.4.fli
<https://drive.google.com/a/lambertinstruments.com/file/d/19NwEUveiphMxUf9QSjtSHSMBthlaPxqW/view?usp=drive_web>

Also have attached a Recording with our New FLIM system, because originally
the .fli was for our FLIM system.
Those files are still compatible. So for testing purposes, I included that
such that you can make sure it still works.
See attachment.

Please let me know if you have any further questions.



Best regards,

Johan Herz, Sales Engineer

Please visit FLIM.camera for more information about the Toggel.

Tel: +31-50-501-8461 | Skype: lambert-johan
Lambert Instruments BV|Leonard Springerlaan 19 (5th floor)|9727 KB
Groningen|The Netherlands
Dutch Chamber of Commerce nr.: 52396940 | www.lambertinstruments.com


Op ma 17 dec. 2018 om 15:41 schreef Sebastien Besson (Staff) <
s.besson at dundee.ac.uk>:

> Hi Aaron,
>
> On 14 Dec 2018, at 10:00, Ponti Aaron <aaron.ponti at bsse.ethz.ch> wrote:
>
> 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.
>
>
> From the internal specification of the LI-FLIM file format which we used
> for the reader [1]:
>
> "The datatype key can have one of the following 8 values: UINT8, INT8,
> UINT16, INT16,
> UINT32, INT32, REAL32 or REAL64.”
>
> A file that would use UINT12 would probably be a new variant of the file
> format for which we
> have currently neither a format specification nor representative samples
>
> 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).
>
>
> Understood. This would be consistent with the pixel type issue reported
> above i.e. that could
> indeed reflect an internal layout different from the one Bio-Formats is
> expecting..
>
>  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.
>
>
> Over the past years, we have been working on ways to have more sustainable
> support for new file
> formats including any variants of existing file formats. We published a
> blog post summarizing our
> experience a few years ago [2] and since then more manufacturers have been
> engaging in this
> process.
>
> Have you been in touch with Lambert Instruments to report this issue? Are
> they aware that the latest files
> produced by their software are no longer readable by Bio-Formats and any
> software based upon it?
>
> Representative samples allowing to reproduce the issue are always welcome.
> Ideally public samples licensed
> under CC-BY license [3] are the most effective way to help spontaneous or
> sponsored contributions to the
> project and facilitate both the immediate software work as well as the
> long-term maintenance.
> You can upload datasets under 2GB to our QA system [4] and we can provide
> FTP credentials for large samples.
>
> Best,
> Sebastien
>
>
> [1]
> https://docs.openmicroscopy.org/bio-formats/5.9.2/formats/lambert-instruments-flim.html
> [2]
> https://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/
> [3] https://downloads.openmicroscopy.org/images/
> [4] http://qa.openmicroscopy.org.uk/qa/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
> T: +41 61 387 33 74
> F: +41 61 387 39 93
>
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>
>
>
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