We're Hiring!

Saving OME.TIF Uncompressed Terribly Slow

Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats
Please note:
Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats

If you are having trouble with image files, there is information about reporting bugs in the Bio-Formats documentation. Please send us the data and let us know what version of Bio-Formats you are using. For issues with your code, please provide a link to a public repository, ideally GitHub.

Saving OME.TIF Uncompressed Terribly Slow

Postby Oli » Tue Nov 27, 2018 3:26 pm

Dear BioFormats,

We we trying to use BioFormats Exporter from Fiji to save as .ome.tiff uncompressed.

For a 400MB image, this took 2.5 minutes! that is, it was saving the data (locally, to an SSD) at 4MB per second...

A tiff is saved in mere seconds.

We are running on Windows 10 on a giant processing machine.

To my knowledge, the openSPIM saves data as ome.tiffs and manages to work much faster than that. So what am I missing, as right now we cannot use ome.tiff even if we wanted to.

Any help is appreciated
Oli
 
Posts: 71
Joined: Mon Nov 29, 2010 4:57 pm

Re: Saving OME.TIF Uncompressed Terribly Slow

Postby sbesson » Wed Nov 28, 2018 4:14 pm

Dear Oli,

thanks for your post. I believe the performance issues you are describing are the same as the ones discussed in this thread on the image.sc forum.

As far as we know, the problem is independent of the operating system or the amount of memory and happens both for plain TIFF and OME-TIFF written by the ImageJ plugin.

With a large portion of our work on pyramidal OME-TIFF and a growing community now getting blocked by this issue, we are prioritizing the investigation of this issue. See this card if you want to follow the ongoing investigation. We will update the various threads when we have a fix into place that is ready to be tested by the community.

Best,
Sebastien
User avatar
sbesson
Team Member
 
Posts: 421
Joined: Tue Feb 28, 2012 7:20 pm


Return to User Discussion [Legacy]

Who is online

Users browsing this forum: No registered users and 1 guest