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

[Will Moore]

Hi Nick,

  One more thing to try, just to use the latest build of Bio-Formats.
You can get this from our automated build site. For LOCI this is

http://hudson.openmicroscopy.org.uk/job/LOCI/

Grab the latest loci_tools.jar there and put in ImageJ plugins folder  
etc...

  Let us know if that helps.
If not, could you send any error message you get when exporting from  
ImageJ fails?

  Cheers,

    Will.



On 8 Sep 2009, at 09:31, Nick Perry wrote:

> 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
>>
>>
>> Genomic Institute of the
>>
>> Novartis Research
>>
>> Foundation
>>
>> 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
>>
>> _______________________________________________
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>> 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
>
>
> _______________________________________________
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William Moore
Division of Gene Regulation and Expression
College of Life Sciences
University of Dundee
Scotland
DD1 5PH

Tel 01382 386364

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