LOCI Import Tile Images Question

[Sebastian Rhode-3]

Hi,

our imaging software (Live Acquisition from TILL Photonics) is capable of acquiring tile images (e.g. X*Y) combined with Z-stacks or muti channel acquisitions over time. As an output format there is the option to use the OME-TIFF format. So let´s assume I acquired a 3x3 tile with just one plane, color and time point.

To open this image set I use the LOCI import. And I checked the "Tile Images" option, since my hope was, that LOCI will tile the images according to the image coordinates, which are saves inside the meta data according to the OME standard. But this does not seem to work. There is no error message, but maybe I just do something wrong.

So is there a way to tile images automatically during the LOCI import according to the image positions? If not, this would maybe a nice feature to have?

Cheers,

Sebi

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[Melissa Linkert-2]

Hi Sebi,

> our imaging software (Live Acquisition from TILL Photonics) is capable of acquiring tile images (e.g. X*Y) combined with Z-stacks or muti channel acquisitions over time. As an output format there is the option to use the OME-TIFF format. So let´s assume I acquired a 3x3 tile with just one plane, color and time point.
>
> To open this image set I use the LOCI import. And I checked the "Tile Images" option, since my hope was, that LOCI will tile the images according to the image coordinates, which are saves inside the meta data according to the OME standard. But this does not seem to work. There is no error message, but maybe I just do something wrong.

I assume you mean the "Stitch tiles" option in the "Bio-Formats Import
Options" window?

If so, that is supposed to work, provided that the coordinates are present
in the file and that it is easy to determine the layout of the tiles
from the coordinates (in general, this means no overlap).

> So is there a way to tile images automatically during the LOCI import according to the image positions? If not, this would maybe a nice feature to have?

If you have the latest version of Bio-Formats (4.4.0, see
http://loci.wisc.edu/bio-formats/downloads) and "Stitch tiles" does not
work, then it would help if you could send a sample file.

Please note though that the "Stitch tiles" option is in no way a replacement
for proper stitching; in all but the simplest of cases, you will need to
use the stitching plugins:

http://fiji.sc/wiki/index.php/Stitching

Regards,
-Melissa

On Mon, Jul 16, 2012 at 03:27:13AM -0400, Sebastian Rhode wrote:

> Hi,
>
> our imaging software (Live Acquisition from TILL Photonics) is capable of acquiring tile images (e.g. X*Y) combined with Z-stacks or muti channel acquisitions over time. As an output format there is the option to use the OME-TIFF format. So let´s assume I acquired a 3x3 tile with just one plane, color and time point.
>
> To open this image set I use the LOCI import. And I checked the "Tile Images" option, since my hope was, that LOCI will tile the images according to the image coordinates, which are saves inside the meta data according to the OME standard. But this does not seem to work. There is no error message, but maybe I just do something wrong.
>
> So is there a way to tile images automatically during the LOCI import according to the image positions? If not, this would maybe a nice feature to have?
>
> Cheers,
>
> Sebi
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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