[ome-users] ome-users Digest, Vol 51, Issue 17 --> stitching channels in to tiff files

[b.gerritsen at nki.nl]

Many thanks Frans!

Your advice helped big time! I can now import separate tiff files as a single multi-channel-image.

Cheers,
Bram
________________________________________
From: Cornelissen, Frans [PRDBE] [FCORNELI at its.jnj.com]
Sent: Thursday, June 18, 2009 9:03 AM
To: Bram Gerritsen; ome-users at lists.openmicroscopy.org.uk
Subject: RE: ome-users Digest, Vol 51, Issue 17 --> stitching channels in to tiff files

Hi Bram,

I have the same issue: combining different channels in 1 tiff file and
import them in OMERO so that Insight shows all the channels combined.
What can be done is to turn the individual TIFF files into OME-TIFF
before
Uploading them to OMERO.
This only means that you embed an XML string into your tiff file; all
tiff readers will still be able to read the file as well.
The XML can specify that a certain tiff file is a channel that belongs
to a group of channels, so they will be imported into OMERO as
one-multi-channel image
Take a look at http://www.loci.wisc.edu/ome/ome-tiff-code.html

Cheers, frans

-----Original Message-----
From: b.gerritsen at nki.nl [mailto:b.gerritsen at nki.nl]
Sent: Wednesday, 17 June 2009 6:03 PM
To: Cornelissen, Frans [PRDBE]; ome-users at lists.openmicroscopy.org.uk
Subject: RE: ome-users Digest, Vol 51, Issue 17 --> stitching arbitrary
tiff files

Thanks Frans!

Despite the helpful answers I discovered that my original question was
not specific to my situation. Stitching together TIFF files using
different programs such as loci.formats.tools.ImageConverter or ImageJ
resulted in a stacked image file where each image represents a different
time-point. However, what I need is that each image represents a
different channel. Does anyone know how can this be accomplished?

Kind Regards,
Bram
________________________________________
From: Cornelissen, Frans [PRDBE] [FCORNELI at its.jnj.com]
Sent: Wednesday, June 17, 2009 9:55 AM
To: ome-users at lists.openmicroscopy.org.uk; Bram Gerritsen
Subject: RE: ome-users Digest, Vol 51, Issue 17 --> stitching arbitrary
tiff files

Hi Bram,

For simple stitching, you can use ImageMagick or JMAgick :
http://sourceforge.net/projects/jmagick/

For non-exactly-matching images, you can use largemontage, also a java
app & handles tiff
http://vtuo.pp.fi/software/largemontage/

hope this helps,
cheers,frans

Message: 1
Date: Tue, 16 Jun 2009 10:33:53 +0200
From: <b.gerritsen at nki.nl>
Subject: Re: [ome-users] OMERO: import image series spread across
        multiple files
To: <ome-users at lists.openmicroscopy.org.uk>
Message-ID: <8C867DC166C8F645BAFC67CD9842ADDA15DB119B at mstr-1.nki.nl>
Content-Type: text/plain; charset="us-ascii"

Thanks Chris and Brian!

When do you think stitching arbitrary tiff files will be supported?

Kind Regards,
Bram
________________________________________
From: Chris Allan [callan at blackcat.ca]
Sent: Monday, June 15, 2009 6:15 PM
To: Bram Gerritsen
Subject: RE: [ome-users] OMERO: import image series spread across
multiple files

Hi Bram,

Then Brian's suggestion is probably the best place to start. We don't
have support for stitching arbitrary TIFFs together I'm afraid.

Thanks.

-Chris

On Mon, 2009-06-15 at 17:41 +0200, b.gerritsen at nki.nl wrote:
> Hello Chris,
>
> I'm trying to import tiff files.
>
> Kind Regards,
> Bram
> ________________________________________
> From: Chris Allan [callan at blackcat.ca]
> Sent: Monday, June 15, 2009 5:22 PM
> To: Bram Gerritsen
> Cc: ome-users at lists.openmicroscopy.org.uk
> Subject: Re: [ome-users] OMERO: import image series spread across
multiple files
>
> Hi Bram,
>
> The Importer certainly does attempt to support image series that are
> spread across multiple files. Which file format are you having
problems
> with?
>
> -Chris
>
> On Mon, 2009-06-15 at 17:16 +0200, b.gerritsen at nki.nl wrote:
> > Dear all,
> >
> > The OMERO.importer (version 4.0.1) gui and cli do not seem to
support the import of image series that are spread across multiple
files. How can one import these image series into omero?
> >
> > Kind Regards,
> > Bram Gerritsen
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>