Reading mosaic images, LOCI?

[Gabriel Landini]

Hi,
This question is mainly for LOCI people but I thought that it might be of
interest to others.

I am considering a system for scanning whole slides based on the OASIS glide
stage.

Does anybody know if there is a way of loading the tiles or a subpart of a
tiled slide that their software produces? (I asked the manufacturer, but they
did not know).

There are some sample images here, in the "FTP_Site" link, under "Workspaces"

http://www.objectiveimaging.com/Download/OI_Download.htm

These are folders full of jpgs (I have been told it can save as TIFFs too) and
some data files with tiles names and coordinates.

I guess that this can be parsed and that LOCI/Bioformats might have the
facility already, but I have not been able to find out how to load these.

Many thanks in advance for any information.

Cheers

Gabriel

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[Melissa Linkert-2]

Hi Gabriel,

> I am considering a system for scanning whole slides based on the OASIS glide
> stage.
>
> Does anybody know if there is a way of loading the tiles or a subpart of a
> tiled slide that their software produces? (I asked the manufacturer, but they
> did not know).
>
> There are some sample images here, in the "FTP_Site" link, under "Workspaces"
>
> http://www.objectiveimaging.com/Download/OI_Download.htm
>
> These are folders full of jpgs (I have been told it can save as TIFFs too) and
> some data files with tiles names and coordinates.
>
> I guess that this can be parsed and that LOCI/Bioformats might have the
> facility already, but I have not been able to find out how to load these.

Bio-Formats does not currently support this particular slide format,
though the fact that each of the individual tiles is stored as a JPEG
file means that you should be able to open the tiles right now with no
problem - they just won't be automatically put together into a slide.

I have also filed a ticket on the OME issue tracker to have Bio-Formats
fully support this data:

http://trac.openmicroscopy.org.uk/ome/ticket/9932

Regards,
-Melissa

On Tue, Nov 20, 2012 at 04:25:53PM +0000, Gabriel Landini wrote:

> Hi,
> This question is mainly for LOCI people but I thought that it might be of
> interest to others.
>
> I am considering a system for scanning whole slides based on the OASIS glide
> stage.
>
> Does anybody know if there is a way of loading the tiles or a subpart of a
> tiled slide that their software produces? (I asked the manufacturer, but they
> did not know).
>
> There are some sample images here, in the "FTP_Site" link, under "Workspaces"
>
> http://www.objectiveimaging.com/Download/OI_Download.htm
>
> These are folders full of jpgs (I have been told it can save as TIFFs too) and
> some data files with tiles names and coordinates.
>
> I guess that this can be parsed and that LOCI/Bioformats might have the
> facility already, but I have not been able to find out how to load these.
>
> Many thanks in advance for any information.
>
> Cheers
>
> Gabriel
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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