[ome-users] Fiji Bio-Formats Exporter Problem - write each timepoint to a separate file

[Balaji Ramalingam (Staff)]

Hi Ofra,

Thank you for reporting your issue.
Testing the same locally, we were unfortunately unable to reproduce the
bug.

I have recorded the Fiji/ImageJ operations that I had performed (using the
Fiji/ImageJ macro recorder) and I have pasted the same here,

run("Bio-Formats Exporter",
"save=/Users/bramalingam/Desktop/FijiExportTest/mitosisOmeTiff/mitosis_time
point_.ome.tif write_each_timepoint compression=Uncompressed²);

I reimported the resultant images back into Fiji/ImageJ and compared the
pixel data with the original image.

There was no obvious issue that was noticed, thus could you please record
your mouse-click operations via the Fiji/ImageJ macro recorder and paste
the resultant command here? The documentation for the same can be found
here,
https://imagej.net/Introduction_into_Macro_Programming#The_recorder


And also it would be great if you could clarify the version of Bio-Formats
that was used? (I have updated my Fiji to use the latest release version
of Bio-Formats : Version 5.3.0)

You can get the same by selecting,
Help‹>About Plugins‹>Bio-Formats PluginsŠ (in the Fiji menu)

Or by running the following macro command,
run("Bio-Formats Plugins...²);

This would help us troubleshoot the issue in better detail.

Best,
Balaji


__________________
Mr Balaji Ramalingam
Software Developer

OME Team
School of Life Sciences
University of Dundee






On 12/12/2016, 14:54, "ome-users on behalf of Ofra Golani"
<ome-users-bounces at lists.openmicroscopy.org.uk on behalf of
ofra.golani at weizmann.ac.il> wrote:

>Hi,
>
>I encounter a problem when using Bio-Formats exporter to save each
>time-point into separate file.
>It saves into separate files, but the files are corrupted. You see this
>when you move through the slices.
>You can try this with the "Mitosis" 5D stack of Fiji Sample files.
>The problem happens when I save files both as tif and as ome.tif.
>I use the latest Fiji version, with the latest Bio-Formats version.
>
>Please advise,
>Thanks,
>
>Ofra
>
>----------------------------------------
>
>Ofra Golani
>
>BioImage Analyst
>Life Sciences Core Facilities
>Weizmann Institute of Science
>Tel: +972-8-934-5177
>ofra.golani at weizmann.ac.il
>http://www.weizmann.ac.il/Biological_Services/units/cell-observatory/about
>-service
>
>
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>ome-users mailing list
>ome-users at lists.openmicroscopy.org.uk
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