Handling CycIF images in OMERO.figure 4

[jcopeland]

Hello,

We have begun using OMERO.figure 4 to create figures based on big tiled pathology images. Thank you for making this possible in version 4!

It would be very helpful if channel name information were available in the preview panel, especially when working with CycIF images which can have dozens of channels. PathViewer now supports channel groups as a way to help organize the channel display in these types of images. It would be fantastic if figure could do this too.

One more observation, it seems that figure cannot handle the URLs of PathViewer images as input to start a new figure. It handles image ids fine. It would be nice, however, if one could set up channel display in PathViewer and have the URL of the resulting image be understood by figure, probably because of the large number of channel settings encoded in the URL. If figure could interpret these URLs this could be a workaround to the problem of not having the names of the channels in the preview pane.

Thanks!

Jay

[wmoore]

Hi Jay,

I don’t know how PathViewer currently groups channels (probably specified in an annotation of some kind). We haven’t yet discussed with Glencoe whether this is a feature that is expected to be supported outside of PathViewer, but we will do.

Showing the channel name in the Preview panel is certainly possible. I’ve created a card for this at https://trello.com/c/QgzoGsmi/195-chann ... view-panel. One question is how much space do we need for names? Long channel names will need to be truncated (as they currently are in iviewer), but how many characters of the name are needed to identify it?

The “Add Images” dialog expect IDs or the URL copied from the Link button in webclient, e.g./webclient/?show=image-4405|image-4406 (for multiple images) and it also supports the main viewer URL http://server.org/webgateway/img_detail/4405/ but it doesn’t support any rendering settings in the URLs.
I don’t know what Pathviewer URLs look like so I haven’t tested.
However, if you save the rendering settings for an Image then those will be used when the Image is opened in figure.

Hope that helps,
Regards,

Will