Saving OME.TIF Uncompressed Terribly Slow

[Oli]

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

[sbesson]

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