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

[Nick Perry]

Nope, I gave up.

Nick

On Tue, Sep 8, 2009 at 10:29 AM, Will Moore <will at lifesci.dundee.ac.uk>wrote:

>  Hi Nick,
>  I just tried this yesterday and also failed to export from ImageJ with
> Bioformats. (Don't remember the error I'm afraid).
> However, I tried again today (possibly with different images) and it seems
> to be working OK (no errors).
>
> Hopefully you've got this to work now?
>
>    Will.
>
>
> On 7 Sep 2009, at 08:12, Nick Perry wrote:
>
> 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
>>
>> __________________________________________
>>
>> Research Investigator
>>
>>
>> *G*enomic Institute of the
>>
>> *N*ovartis Research
>>
>> *F*oundation
>>
>> Department of Informatics, room C117
>>
>> 10675 John Jay Hopkins Drive
>>
>> San Diego CA 92121
>>
>> USA
>>
>>
>> +1 (858) 812-1534 (W & F)
>>
>> +1 (757) 941-4194 (H)
>>
>> +1 (858) 354-7388 (M)
>>
>> www.gnf.org
>>
>>
>> *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
>>
>> _______________________________________________
>> ome-devel mailing list
>> ome-devel at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>>
>>
>
> <bio-formats_error.tiff>_______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
>
>  William Moore
> Division of Gene Regulation and Expression
> College of Life Sciences
> University of Dundee
> Scotland
> DD1 5PH
>
> Tel 01382 386364
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20090908/f8b4fab8/attachment.htm