[ome-users] Maximum size supported in OMERO Importer

[Chris Allan]

Just to elaborate based on our experiences with "very large" images  
here at Dundee. We currently deal with 5-dimensional (XYZCT) datasets  
greater than 10GB in a variety of microscopy data formats. Though the  
largest 2-dimensional sections/planes/frames we deal with regularly  
are 1024x1024; this excludes so called "stitched" images.

As very large 2-dimensional sections/planes/frames are something we  
are likely to tackle early in the new year we'd certainly welcome any  
feedback, experiences or use cases. Particularly 2048x2048 or greater.

Thanks.

-Chris

On 11 Dec 2008, at 22:48, Chris Allan wrote:

> Hi Sriram,
>
> As "image" is a rather loaded term would it be possible for you to
> qualify exactly what you mean? How large are these 25MB JPEGs
> physically? 4096x4096 or greater across the X and Y dimensions? OMERO
> is currently quite poor in its support of very large 2-dimensional
> images. The memory overhead in Bio-Formats is also quite high for very
> large 2-dimensional JPEGs.
>
> TIFFs would likely give you better performance.
>
> Hope that helps.
>
> -Chris
>
> On 11 Dec 2008, at 19:17, Nandakumar, Sriramkumar wrote:
>
>> Hi Brian,
>> Thanks for the reply.
>> We are trying to upload large image size of around 300 MB in Omero
>> Importer.
>> However it is not possible for us to upload JPEG image of 25 MB in
>> Omero. The importer shows the status as "Analyzing".
>> Since for our research we are dealing with large image sizes of more
>> than 100 MB we are finding very difficult to upload images.
>> Is there any other image format which is compatible with Omero for
>> better uploading?
>>
>> Thanks in Advance.
>>
>> Thanks & Regards,
>> Sriram.
>> ________________________________________
>> From: Brian Loranger [brian.loranger at lifesci.dundee.ac.uk]
>> Sent: Thursday, December 11, 2008 5:30 AM
>> To: Nandakumar, Sriramkumar
>> Subject: Re: [ome-users] Maximum size supported in OMERO Importer
>>
>> Hmm.. tricky question.
>>
>> The importer is set to use up to a gig of available RAM on your
>> machine. What that translates to in terms of 'how big of an image'
>> however is very dependent on what format is being imported.
>>
>> If your importing a simple format with little metadata, (like a
>> basic tiff image), this should allow you to import images where each
>> plane is about 500 megabytes in size. (there's only a small
>> additional overhead for organizing multiple planes). More metadata
>> rich formats will lower the amount of available memory available for
>> the plane import process, but it shouldn't be too excessive.
>>
>> Are you asking this question because you have a specific importing
>> problem?
>>
>> Cheers,
>>
>> Brian Loranger
>> Software Developer, Open Microscopy Environment
>> Division of Gene Regulation and Expression
>> University of Dundee
>> (The University of Dundee is a registered Scottish charity, No:
>> SC015096)
>>
>>
>>
>>
>> On 11 Dec 2008, at 01:29, Nandakumar, Sriramkumar wrote:
>>
>> Hi,
>> I would like to know what is the maximum image size that can be
>> uploaded in Omero Importer?
>> Could anyone appraise me the above info?
>>
>>
>> Thanks in Advance.
>>
>>
>> Thanks & Regards,
>> Sriram.
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