Open Microscopy Environment

Hello, I installed today the virtual image of omero, and I'm quite impressed by the software.
I'm interested mainly in the export function till know. I have microscopy images (drosophila eyes) but the ROI export tool is not very useful because it shows all the channels.

There is surely a way to script a different export routine, but is there also a setting somewhere in the GUI?

Hi Mario,

When you say "ROI export tool" do you mean the "ROI split figure..." option?

You should be able to turn off individual channels for this. In the attached screen-shots I have chosen to show only the blue and green channels - the red channels are turned off. The selection buttons are below the channel names.

You can of course edit the script to customize it further, since this ROI figure is using the scripting service http://trac.openmicroscopy.org.uk/ome/wiki/OmeroScripts but hopefully the GUI does what you want for now?

Cheers,

Will.

Yes, I already tried this, but because I have a color picture of an eye (not fluorescence), if I turn off one of the RGB channels, the color of the picture will not be correct anymore.

Ah - OK, I understand now.

Can you give me a few more details on the functionality you'd like?
Is it closer to "Batch Export Images" http://www.openmicroscopy.org/site/supp ... l-scripts/ (see movie).

It should be fairly straight-forward to add functionality to this script to export ROI regions and/or the full planes.

Or do you want the ROI Split Figure to work as it does now, but to allow you to turn all the channels off, so that you only get the full plane and the merged ROI region? (currently, if you turn all the channels off, then it automatically turns them all on again).

Cheers,

Will.

Yes, the last possibility would be my favorite.
That you get the merge in the full window, and the merge also in the magnified ROI.

I've updated the script to not show any split channels (if you turn them all off). Here's a figure I made, with all the channels turned ON in the merged panels.

I've attached the script. If you're not an admin on your server, you'll have to get an admin to upload it to replace the existing script in dist/lib/python/scripts/omero/figure_scripts/ROI_Split_Figure.py. I should say that it's not been tested thoroughly yet, so you should keep a copy of the existing one. But hopefully I won't have added any bugs.

Let me know if this is working for you - then we can add it to the next release.

Cheers,

Will.

Thank you, it works fine.

Just for interest, is there a possibility to show more ROIs in the export function?

In my case: I have two flies on one image, I'm interested in the eye color. One one side there is the big image, and then I show the two ROIs with magnification on the side (maybe labeled with the name of the ROI).

Thanks a lot!

The problem is that as soon as you display multiple ROIs it kinda becomes a different figure: E.g.

- Do you care about the order of the ROIs? You'd want the left eye to the left? How do you want to sort them? Alphabetically by text label? By ID?
- What if someone chooses to show multiple ROIs AND wants multiple channels (as in the original Split ROI)?

I think the layout you describe could be a generally useful figure, so I'll try and have a go at it, when I get the time. But I really want to improve the figure scripts a bit first, to factor out all the code that does the laying out of the panels and labels. The existing scripts have a ton of code that does this and it means changing them or writing new scripts takes a while.

So, no promises I'm afraid. Things are pretty busy just now, but if you'd like to attach a figure that shows what you'd like, that would be a big help.

Thanks,
Will.

No problem.

I was thinking about something similar to the image attached.

For fluorescent figures, I could imagine, that it would be useful, if you show the splitchannels also ordered by ROIs (so for example ROIs ordered horizontally, and channels vertically).

I personally don't really care in which order the ROIs are. I think I could live with the ID order.

Maybe once I have a look to the code, and maybe try myself to code something like this, but at the moment I'm pretty absorbed by my wet lab work.