[ome-devel] Compression in OME-TIFF file?

[Nick Perry]

So I can't actually get the ImageJ plugin for bio-formats to actually
work... Every time I import an image either with the LOCI tool or the
standard ImageJ 'open' and try to export it, I get errors. I've tried
playing around with the import options as well (splitting channels into
separate images, etc). I've attached one of the error messages as an image.
Anyone know how to actually get this to work..? I've tried opening .ome.tif
files and a .jpg.

Nick

On Fri, Sep 4, 2009 at 6:15 PM, Ghislain Bonamy <GBonamy at gnf.org> wrote:

>  Nick,
>
>
>
> I am sure you are aware of this, but though I would point this out anyways.
> The JPEG200 compression is a lossless compression (not like regular JPEG).
> The advantage of LZW over JPEG2000 is that the image can still be read by
> other image readers. On the flip side JPEG2000 will give you much better
> compression of your data (in particular if your data is complex), but the
> image will only be correctly handled by Bio-Formats.
>
>
>
> Best,
>
>
>
> Ghislain Bonamy, PhD
>
> __________________________________________
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> *From:* ome-devel-bounces at lists.openmicroscopy.org.uk [mailto:
> ome-devel-bounces at lists.openmicroscopy.org.uk] *On Behalf Of *Curtis
> Rueden
> *Sent:* Friday, September 04, 2009 6:56 AM
> *To:* Nick Perry
> *Cc:* ome-devel at lists.openmicroscopy.org.uk
> *Subject:* Re: [ome-devel] Compression in OME-TIFF file?
>
>
>
> Hi Nick,
>
>
>
> You can generate one using the Bio-Formats Exporter plugin for ImageJ.
>
>
>
> First, open any image. Then choose Plugins > LOCI > Bio-Formats Exporter,
> save as OME-TIFF format, and a dialog box will appear allowing you to select
> the compression type—give either "LZW" or "JPEG2000" a try.
>
> The compression will change nothing about the embedded OME-XML, only how
> the TIFF planes are stored in the file. And all OME-TIFF compression is
> plane by plane (i.e., no compression over a 3D block of pixels).
>
>
>
> -Curtis
>
>
>
> On Fri, Sep 4, 2009 at 4:16 AM, Nick Perry <nperry at stanford.edu> wrote:
>
> Hi,
>
> Does anyone know where I can download an example OME-TIFF file that is
> compressed? I see on the LOCI site (
> http://www.loci.wisc.edu/ome/ome-tiff-data.html) that it is possible to
> compress the data in an OME-TIFF file, like with LZW for example, and I'm
> trying to find out where in an OME-TIFF file the compression is specified.
> (This all hinges of course on my intuition that it is the raw image data
> that is compressed, and not the surrounding tiff structure/ome-xml block.)
>
> Thanks,
> Nick
>
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> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
>
>
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