[ome-users] export ics 1.0

[Dudok Barna]

Dear Andrew,
 Thanks for your fast and kind reply!
 Indeed, form ImageJ, calling with '.ids' filename just creates the same ics v2 file with .ids extension in the filename.
 I've tried the workaround, but it didn't work. In your shell output it's also apparent that the resulting .ics is small and the .ids is large. I've renamed the 2 files to swap the extensions, but they can't be opened by any software (imagej just does nothing, NIS Elements crahes).
Yours,
Barna

----- Original Message -----
From: "Andrew Patterson" <ajpatterson at lifesci.dundee.ac.uk>
To: "ome-users at lists.openmicroscopy.org.uk OME-Users" <ome-users at lists.openmicroscopy.org.uk>
Sent: Thursday, July 3, 2014 12:38:52 PM
Subject: Re: [ome-users] export ics 1.0

Hello Barna,

The ics writer code chooses which version of the file to write based on the file extension chosen for the output filename.

If you save as filename.ics a single V2 file is produced "filename.ics".
If you save as filename.ids a two V1 files are produced "filename.ids" & "filename.ics".

Having said that when we tested this using bio-formats from within imagej we could not get the ids version to work.

There is however a workaround.

If you download the bftools package you can perform the conversion with `bfconvert`
https://www.openmicroscopy.org/site/support/bio-formats5/users/comlinetools/index.html

If you run
./bfconvert yourInputFile outputFile.ics
You get:
-rw-r--r--  1 andrew  andrew  1539962  3 Jul 11:17 outputFile.ics

If you run
./bfconvert yourInputFile outputFile.ids
You get:
-rw-r--r--  1 andrew  andrew      389  3 Jul 11:17 outputFile.ics
-rw-r--r--  1 andrew  andrew  1539573  3 Jul 11:17 outputFile.ids

Hope this helps,

Andrew

On 3 Jul 2014, at 10:34, Dudok Barna <dudok at koki.hu> wrote:

> Hi All, 
> 
> Sorry if this should be obvious, but I searched in vain, I hope I can get some help here...
> I'd like to save images from imagej macro using the Bio-Formats Exporter plugin.
> The output file is in ics 2.0 format, which cannot be read by the software i need to open it with.
> The LOCI Bio-Formats documentation says that ics 1.0 and 2.0 are both supported. How can I save the file in ics 1.0 (.ics, .ids file pair) format?
> Thanks for your help!
> Barna
> 
> Barna Dudok
> Institute of Experimental Medicine
> Hungarian Academy of Sciences
> 43 Szigony str.
> H-1083
> Budapest
> HUNGARY
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

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