Open Microscopy Environment

My lab deals heavily with multi-channel LSM files from a Zeiss LSM 710. I love being able to import them into Omero and playing with them, but there is one thing that bothers me. It would be of great benefit for us to be able to label the channels with the associated antibody names in Omero. For instance, I'd like to be able to see these edited channel names in the Image Viewer. I've looked around the client and your forums to find something, and I haven't really seen a straight answer.

I can imagine that one possible solution would be to save all the channels as individual TIFFs, then re-import and combine using your CombineImages script (and adding channel names there), but we will be importing a large number of images and the time/resources needed for that wouldn't be feasible.

I'm not at all familiar with Python, but I suppose I could start looking in to writing a script for this if need be. If anyone has an easier answer, though, I'd greatly appreciate it.

Thanks!

Hi,

It's funny because today we were just discussing that Insight and OMERO.web should support Channel renaming...

Anyway, I just took the Channel naming code from Combine_Images and put it into a new Rename_Channels.py script.

You can see it at https://gist.github.com/3997000

This works on selected Images or whole Datasets. You just enter a comma-separated list of channel names, E.g.

DAPI, FITC, Texus-Red

Hope that helps,

Will.

Yes, that's exactly what we needed. I've tested it out with both .LSM and .CZI files and it works great. I was thinking about trying to cut out that piece of code and putting it into a new script, but...it would have taken me much more time than it took you. You guys are awesome. Thank you!