[ome-users] Question about IMS format importing from metasystems slide scanners

[Chris Allan]

Hi JC,

On 6 Aug 2012, at 07:06, Jake Carroll wrote:

> Hi all.
> 
> We're having problems with the Omero importer (through insight). Effectively, we've been able to import several formats in testing thus far, but we've reached a stumbling block.
> 
> It seems that the importer hangs indefinitely with files that are generated with .IMS files (from Metasystems software) that runs our high throughout slide scanners. These IMS files are extremely large 2D multichannel XY images (although can be 3D as well). IMS files are typically used for 3D datasets so perhaps OMERO is not expecting them to contain the large amounts of 2D data?

Sorry to hear that. When you say "extremely large" what are the actual dimensions? While it may appear that the importer is "hung" it can take several hours to properly process a very large 2D image as an image pyramid is being built on the fly.

> 
> It's unusual, because I don't think there is anything wrong with the header as some tools we use such as Bitplane's Imaris can open them without trouble, as can the LOCI bioformats plugin.
> 
> Any thoughts? Any logs you'd like me to look at, or any specific debug?

Outside of the information above about the only thing useful would be an example of the file itself.

> 
> Thanks, all!
> 
> --JC

-Chris