Open Microscopy Environment

Hello,


One user recently pointed out that the "split view figure" script generates weird colors and does not take those from the image into consideration.
It seems the colours are ok when the script is started from the web though.
Also, in both cases, the name of the first channel mostly becomes a black rectangle...

Is it something specific to our server... ?

Hi,
I've reproduced the bug in Insight, so we'll look into that...

For the black label, it looks like this is caused by a bug in the rotation of the vertical left label.
This is only an issue when using version 3.1.0 of Pillow (and probably future versions).
I've created a card to fix this https://trello.com/c/rE4VXlX1/33-figure ... labels-bug as we have already done in OMERO.figure: https://github.com/ome/omero-figure/pull/140. However this won't be in time for the imminent 5.3.3 release of OMERO.
In the meantime, you could try to install an older version of Pillow (2.9) as a workaround to see if that fixes the issue (as noted on the PR above).

Regards,

Will.

I've created a fix for the labels in https://github.com/ome/scripts/pull/135
Although that is unlikely to make it into the 5.3.3 release, once it is tested and merged, you could replace your script with the latest in

Code: Select all

lib/scripts/omero/figure_scripts/Split_View_Figure.py


Regards,

Will.

Thank you!

Hi,
with Wills help I finally managed to replicate the false color issue when the script is called from Insight.
It should be a simple fix, but like the labels bugfix, it's unlikely to get into the upcoming 5.3.3 release.
Regards,
Dominik