Open Microscopy Environment

Hello,

we have noticed bugs with the Omero plugin since the last update (5.4.10).

when we export the figure in pdf format, the scale bar looks thicker.

also when we export in tiff format, the text font changes.

Thank you in advance for your help

Sameh

Hi Sameh,

The version of OMERO.figure you're using is independent of the OMERO server version.
The last release of OMERO.figure was 4.0.2 but you may or may not have updated that when you last updated OMERO to 5.4.10.

I tried exporting a figure with the latest export script and with an older script (from 3.0.0) but I didn't see any difference in scalebar thickness, and when I inspect the thickness by opening the PDF in Adobe Illustrator I see that they are '3pt' in the latest and the older export. Can you measure the thickness? Are you sure it doesn't simply appear thicker because of different sized panels or page?

The fonts used by PIL for TIFF export are loaded from the OMERO dist at
OMERO.server/lib/python/omero/gateway/pilfonts/FreeSans.ttf
Can you check to see if that font is there (along with FreeSansBold.ttf, FreeSansOblique.ttf and FreeSansBoldOblique.ttf).

Let us know if that helps?

Regards,
Will.

hello,

our omero figure version is 4.0.2.

About the fonts, they are in the correct directory.

I made screenshots to show you the differences between Omero figure and PDF/tiff export.

here is the link to download the screenshots:

https://we.tl/t-zf6C4JzIzk

thank you so much for your help

Sameh

Dear Sameh,

From your OMERO.figure installation environment could you share with us the output of "pip freeze" in case the clue to the problem lies in the version of a dependency?

Cheers,
Mark

mtbc wrote:Dear Sameh,

From your OMERO.figure installation environment could you share with us the output of "pip freeze" in case the clue to the problem lies in the version of a dependency?

Cheers,
Mark

Hello,

below the output of "pip freeze" :


chardet==2.3.0
Django==1.8.19
django-pipeline==1.3.20
django-redis==4.8.0
futures==3.2.0
gunicorn==19.9.0
importlib==1.0.4
Jinja2==2.8
Markdown==2.6.6
MarkupSafe==0.23
numexpr==2.4.3
numpy==1.15.1
omero-figure==4.0.2
omero-gallery==3.1.1
omero-iviewer==0.5.0
omero-marshal==0.5.3
Pillow==3.3.3
Pygments==2.1
PyYAML==3.11
redis==2.10.6
reportlab==3.4.0
tables==3.2.2
virtualenv==15.0.1
zeroc-ice==3.6.4

Thanks Sameh for the information
We need to investigate the source of the problem. I have not been able to reproduce it yet

Cheers

Jmarie