Open Microscopy Environment

Hi OMERO folks,

I am wondering whether large size of ndpi format would be supported near future.

Almost of half of images for our dataset are ndpi images for us (emory univ.) , and it is difficult to tile and customize ndpi images. It's very urgent issue for us.

I found out that this issue has high priority throughout omero ticket web site. But, I don't know what's the current status for this issue ?

It would be great if I know someone who actually handle this issue.

I couldn't find contact information.

Thanks,
Steve

Hi Steve,

I am wondering whether large size of ndpi format would be supported near future.

Yes, they will. However, the technical work required to support this is very definitely not easy.

Almost of half of images for our dataset are ndpi images for us (emory univ.) , and it is difficult to tile and customize ndpi images. It's very urgent issue for us.

I found out that this issue has high priority throughout omero ticket web site. But, I don't know what's the current status for this issue ?

I assume you mean this ticket:

http://trac.openmicroscopy.org/ome/ticket/5092

The status is: we know it needs to be done, but it requires far more time and effort than we have to spare for the next release (4.3.2). The hope is to have it done for the following release, though an actual timeline has not yet been established. To give you an idea of the scope of work involved, we are honestly considering that the easiest solution might be to implement our own JPEG decoder from scratch.

If you would like to receive an email each time that ticket is updated, please PM me with a valid email address and I will CC you.

It would be great if I know someone who actually handle this issue.

I couldn't find contact information.

It is best if you contact us through the forums and/or mailing lists, rather than contacting individual developers - that way, anyone else who is wondering about this same issue can benefit from the response.

Regards,
-Melissa

Hi Melissa,

Thanks for your response.
I appreciate your answer, and I hope to join email lists.
My email address is taewooko@gmail.com

Thanks,
Steve

Hi Steve,

You have now been CC'd on ticket #5092, so you will receive an automated email with "[OME #5092]" in the subject line whenever the ticket is updated. A new trunk build of Bio-Formats that fixes the problem will be available approximately one hour after the ticket is closed ("resolution: => fixed" will appear in the body of the email).

Regards,
-Melissa

Thanks for your inviting of mailing lists.

Thanks,
Steve

Hi Melissa,

I'm also working with ndpi files. Are there news in the integration of the ndpi file format? As I understand, the main problem is that ndpi contains a JPEG stream and JPEG is limited to a maximum image size of 65535×65535 (see http://en.wikipedia.org/wiki/JPEG).

Could you add me as CC on ticket #5092?

Kind Regards,
Andi

Hi Andi,

I'm also working with ndpi files. Are there news in the integration of the ndpi file format? As I understand, the main problem is that ndpi contains a JPEG stream and JPEG is limited to a maximum image size of 65535×65535 (see http://en.wikipedia.org/wiki/JPEG).

Unfortunately, no, there is no news at this point. The two main problems are:

• The JPEG specification only allows for images up to 65500 x 65500, so images larger than this cannot be opened by standard JPEG decoders.
• The JPEG decoder that we are currently using does not allow tile-based access of images; that is, to read even a very small portion of the image, the entire image must first be decoded. We have partially worked around this, but it is incredibly slow and requires a lot of memory.

Could you add me as CC on ticket #5092?

Done (using the email address in your profile). As explained above, you will receive an automated email each time we update the status of the ticket.

Regards,
-Melissa

Thanks