[ome-devel] OME-TIFF merge

Wed Sep 12 19:37:10 BST 2012

Hi,

I have a similar question to the one below which I found on the ome-users list.

My data is ome-tif, and I have different images with several channels. I would like to merge one or more of each to a resulting ome-tif, also copying the according metadata. Is there a plugin out there that does this?

The route I found was to use LOCI channel splitter, convert to a hyperstack, and then merge in there. That does not keep the metadata, though, I fear.

For writing a plugin myself, my questions would be

-    Can IMetadata give me the complete "channel" metadata? Or should I cut it out of the xml string?

-    Is there a more intelligent way of copying a whole channel than to go through all frames and z-positions and do it pixelwise via stack.setVoxel? (I did find the ImageProcessor.getPixels() but did not understand how to use its return value)

And more generally, I sometimes feel that I fail to know basic methods and utils within the loci / bio-formats framework. Are there collections of ome-tiff plugins around (more than those in ImageJ->plugins->Loci and components/loci-plugins/utils)? Also, is there a guide/introduction on how to do things? I often write things that work but at the same time guessing there might be a useful class I don't know of that would make it more elegant...

Best

   Heinrich

Melissa Linkert melissa at glencoesoftware.com <mailto:ome-users%40lists.openmicroscopy.org.uk?Subject=Re%3A%20%5Bome-users%5D%20Combine%20two%20tif%20to%20a%20multilayer%20tif&In-Reply-To=%3C20120514180726.GC31887%40medusa%3E>
Mon May 14 19:07:26 BST 2012

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Hi Jürgen,

> I have some image data in MetaMorph format. The Image format is not

> supported by Omero and I have to create an OME-XML header prior to

> importing the data.

MetaMorph data is definitely supposed to be supported.  Could you please

tell us what goes wrong when you try to import it into OMERO (as the

simplest solution is almost always to just import the original data)?

> Each channel (I have two, DAPI and GFP) is saved in a single separate image.

>

> For further processing I would like to combine the two channel

> images into a multi-layer tif file with a single header.

>

> I can do using convert from the imagemagick pckage:

>

> convert file1.tif file2.tif output.tif

>

> But that literally just concatenates the two files, resulting in a

> multi-layer file but also in two headers, so I have

>

> Exif.Image.Description

>

> as well as:

>

> Exif.Image2.Description

>

> Does anyone know of a tool to properly combine the two tiff files

> resulting in a new multi-layer tif file with a single header?

I believe this:

http://www.imagemagick.org/Usage/color_basics/#combine

and this:

http://www.imagemagick.org/discourse-server/viewtopic.php?f=1&t=13534

explain how to do what you want in ImageMagick.

Regards,

-Melissa

On Mon, May 14, 2012 at 06:15:24PM +0200, Dr. Juergen helmers wrote:

> Hi!

>

> I have some image data in MetaMorph format. The Image format is not

> supported by Omero and I have to create an OME-XML header prior to

> importing the data.

>

> Each channel (I have two, DAPI and GFP) is saved in a single separate image.

>

> For further processing I would like to combine the two channel

> images into a multi-layer tif file with a single header.

>

> I can do using convert from the imagemagick pckage:

>

> convert file1.tif file2.tif output.tif

>

> But that literally just concatenates the two files, resulting in a

> multi-layer file but also in two headers, so I have

>

> Exif.Image.Description

>

> as well as:

>

> Exif.Image2.Description

>

> Does anyone know of a tool to properly combine the two tiff files

> resulting in a new multi-layer tif file with a single header?

>

> Thanks Juergen

>

> --

> *Dr. Jürgen Helmers*

> /Chief Developer/ | webnow | http://www.web-now.de

> *email:*juergen.helmers at gmail.com<http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users> | *tel:*+49 30 37301306 | *skype:*

> helmerj

> _______________________________________________

> ome-users mailing list

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