Resampling in PDF does not seem to work

Hello all,

we have Omero.figure 4.0.2 installed on a local server. For a recent publication we had images that we had to zoom in a lot in the figure so the dpi was around 30. When exporting the figure as PDF, we had large pixels in the low dpi images while the ones with higher “innate” dpi were fine. Then we tried exporting as TIFF (300dpi) and everything looked fine.
Upon checking the dpi export settings, we saw that it was set to 300dpi export. We also tried 600dpi but the PDF looked the same.
Did anyone have a similar problem or could help with this?

Hi, and welcome to image.sc!

When you say you saw the export settings were set to 300dpi, do you mean in the Info panel “Set dpi” for the selected panel, like this:

If so, then that should result in the panel being resampled before being inserted into the PDF. Can you try exporting as “PDF with images”?
This should give you a zip file containing several directories. The 3_final directory contains the images that were inserted into the PDF and these should be resampled. You should also see a 2_pre_resampled directory containing the image before it was resampled.

I find that the PDFs with and without resampling don’t look very different in Mac “Preview” app because it looks like Preview app is doing it’s own re-sampling. But you’re seeing no resampling in both cases?
It’s possible to use a tool like Illustrator to check the DPI (e.g. https://swainhart.org/how-to-check-the-dpi-of-an-image-in-adobe-illustrator-cs5/).

Hope that helps? Let us know,
Will.

Thank you a lot for your quick reply!

Yes, I meant to “Set dpi” to 300 using the Info panel. I exported with images, however there was not folder 2_pre_resampled, only 1_originals and 3_final. I checked the dpi in the PDF using Affinity Designer and it said 31dpi (see attached image). In Designer it looked worse than in Preview.

I then retried on a server with Omero.figure 4.2.0, here everything worked flawlessly. I got all three folders when exporting with images, the dpi in Affinity Designer showed 300 and the image looked fine. Before I wrote the original post I checked if something changed from version 4.0.2 to 4.2.0 but did not see any changes regarding the quality of PDF export. Guess we will just update the 4.0.2 server to the current version.

Designer_dpi.tiff (657.4 KB)

Sorry, I can’t think what the problem is with your older OMERO.figure.

The latest OMERO.figure 4.2.0 requires python 3, Django 1.11, OMERO.server 5.6.0 and omero-py 5.6.0. See Release of OMERO 5.6.0 with Python 3 and
https://docs.openmicroscopy.org/omero/5.6.0/sysadmins/python3-migration.html

We encourage you to update as soon as possible, but in the meantime you might find that installing OMERO.figure 4.1.0 might help. NB: make sure you upgrade the Figure_To_Pdf. export script when you upgrade the app.

Regards,
Will.

No worries, we will just update the older version. We updated last october just before OMERO.figure 4.1.0 but will just jump to 4.2.0. Our server admin will be back on monday.

Thanks again for your help and have a nice day.

Best,
Manuel

Quick update after the version upgrade:
Everything works fine and export with images yields 3 folders with correctly resampled images.