[ome-users] intensity scaling problem when saving a .dv file

[Melissa Linkert]

Hi Kai,

> I am having a curious problem when saving a 16-bit *.dv file (ID 17471 on
> your sever). Please find below the code to see what exactly I did.
>
> In brief I open the raw data with the BF-importer, split the two channels,
> close channel 0 and export channel 1 using the BF-exporter.
>
> When I then open the just saved image using the BF-importer, it appears to
> be on a different intensity-scale (see attached screenshot).

Thank you for the detailed report - I can reproduce this problem with
Bio-Formats 5.3.0.

The issue is that the original file has pixel type int16 (signed
16-bit), which is transformed to uint16 (unsigned 16-bit) during
export.  We have a proposed fix here:

https://github.com/openmicroscopy/bioformats/pull/2696

but until there is a released fix you may be able to work around the
problem by adding this to the macro after the exporter plugin is run:

selectWindow("resaved_data.tif");
run("Calibrate...", "function=[Straight Line] unit=[Gray Value]
text1=[32768 65535] text2=[0 32767] show");

Alternatively, the 'bfconvert' command is not affected by this
problem, so you could instead convert the file to TIFF like this:

bfconvert -range 1 1 raw_data.dv resaved_data.tif

Regards,
-Melissa

On Tue, Dec 13, 2016 at 5:14 AM, Kai Schleicher
<kai.schleicher at unibas.ch> wrote:
> Hi,
>
> I am having a curious problem when saving a 16-bit *.dv file (ID 17471 on
> your sever). Please find below the code to see what exactly I did.
>
> In brief I open the raw data with the BF-importer, split the two channels,
> close channel 0 and export channel 1 using the BF-exporter.
>
> When I then open the just saved image using the BF-importer, it appears to
> be on a different intensity-scale (see attached screenshot).
>
> My guess is that there's something wrong with the raw data since this
> problem appears when using the BF-exporter as well as when using FIJIs own
> "save as -> tiff". The problem also appears when exporting as ome-tiff
> rather then tif.
>
> Thanks for your help and cheers,
> Kai
>
> -------
> run("Bio-Formats Importer", "open=/home/kai/DATA/IMCF/raw/raw_data.dv
> autoscale color_mode=Default rois_import=[ROI manager] split_channels
> view=Hyperstack stack_order=XYCZT");
> selectWindow("raw_data.dv - C=0");
> close();
> wait(1000); // imagej-voodoo
> selectWindow("raw_data.dv - C=1");
> run("Bio-Formats Exporter", "save=/home/kai/DATA/IMCF/raw/resaved_data.tif
> compression=Uncompressed");
> run("Bio-Formats Importer", "open=/home/kai/DATA/IMCF/raw/resaved_data.tif
> autoscale color_mode=Default rois_import=[ROI manager] view=Hyperstack
> stack_order=XYCZT");
> selectWindow("raw_data.dv - C=1");
> run("Histogram");
> selectWindow("resaved_data.tif");
> run("Histogram");
> selectWindow("raw_data.dv - C=1");
> resetMinAndMax();
>
>
>
> --
>
>>> Please note my NEW PHONE NUMBERS: +41 61 207 57 31 (direct) +41 61 207 22
>>> 50 (central)<<
>
> Kai Schleicher, PhD | Research Associate in Advanced Light Microscopy |
> Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel |
> Phone: +41 61 207 57 31 (direct) +41 61 207 22 50 (central) |
> kai.schleicher at unibas.ch | www.biozentrum.unibas.ch |
> www.microscopynetwork.unibas.ch
>
>
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