[ome-users] Images from ROIs script

[William Moore]

Hi Mike, 		(I've cc'd the users list in case anyone else has useful advice or would benefit from this).

 You can configure this as described here: https://www.openmicroscopy.org/site/support/omero5/sysadmins/grid.html#ice-messagesizemax

However, if you have a very large ROI (over approx 3000 x 3000 pixels) then the current script will fail when it tries to create a new image,
since "Big" images over this threshold are tiled and cannot be created from a single plane at a time.

This was discussed at length on our forums (which starts with the same error you have) at
https://www.openmicroscopy.org/community/viewtopic.php?f=6&t=7565

And concludes with a modified version of the script which you can find at:
https://github.com/ebbwdan/omero_scripts/blob/master/omero/util_scripts/Slide_Scanner_Images_From_ROIs.py

So maybe give that script a try - although no guarantees it'll work for your images since it may not have
been tested as much as the "official" released scripts.


 Hope that helps,

   Will.



On 20 Jan 2015, at 16:49, Michael McFarland <Michael.McFarland at jax.org> wrote:

> Hello, Will –
> I got your email address from the Python script.  I run the script but can’t
> find any images afterwards.
>  
> Here is my situation:
> Project: KOMP
> Dataset: ABR
> Image ID: 7532
> ROI: I have two. One rectangle
> I have a dataset named From_ROIs
>  
> I run the script and the log shows:
>  
> unknown = Ice::MemoryLimitException
> Ice.MemoryLimitException
>     reason = "requested 139264030 bytes, maximum allowed is 67108864 bytes (see Ice.MessageSizeMax)"
>  
> Is there a way I can configure this?
>  
> Thanks!
>  
> - Mike
>  
> The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
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