Feature request: Segment multiple channels at a time

Hi there!

Currently, if one is working with multiple channels, the cells in each channel must be segmented by changing the fluorescence channel and segmenting one channel at a time.

This quickly becomes very tedious.
Would it be possible to simply choose the segmentation parameters for each channel in the same window (without having to use the drop-down menu) and then perhaps implement a button to segment both channels at the same time?
The current button (segment cells) intuitively suggests (to me, at least) that the entire image is being segmented with the current parameters. This also leads to some confusion, when one channel has been segmented while the other has not, without any way of knowing other than changing channel (in a different drop-down menu) and loading the segmentation results.

If the multichannel segmentation is not possible, could the two fluorescence channel dropdowns (image preview and segmentation) at least be interlocked? I don’t have any experience with GUI design in Matlab, so I don’t know how many hoops you have to jump to connect elements between panels.
A different idea perhaps, could be a panel to see if the segmentation files have been created (or maybe, which files have been created at all).


Hi Mark,

first of all, I am surprised to hear that the channel drop-down menus are not interlocked, because they should be, and they are for me. Can you please double-check that and send me a screenshot marking the drop-down menus you are referring to (to make sure that we´re talking about the same menus here)?

The reason why channels are not segmented simultaneously is that the parameter settings can be very different between channels, which is why we wanted to keep them separated. In most of our use-cases it is also not necessary to segment all channels, for example when one channel contains a constitutive signal while others represent reporter signals. Finally, I am not sure how the GUI should be organized to choose settings for multiple channels at once.

Actually, there is a way to see if segmented files are available - of you scroll to the right in the table showing the files, there are checkboxes indicating this (see screenshot below). However, this is only regarding the currently loaded channel.


Might I suggest that instead of automatizing the segmentation for several channels at once, you take advantage of the batch processing to automatize the processing of several folders at a time? In the end, I think this will be even more of a game changer regarding tedious button clicks and waiting times. I am happy to walk you through the possibilities of the basic as well as advanced batch processing if you have any questions about it. Especially the advanced batch processing offers a lot of options since you can load a specified parameter file (meaning you can save the settings for each channels under different names, making it much easier to go back and forth), but I understand that it can be a bit overwhelming when getting started, so please don´t hesitate to ask if anything should be unclear.

Let me know what you think - I am looking forward to your reply :grinning:



Hi Hannah,

That clears up some confusion, thank you!
I was just about to test out your advanced batch processing options, I’ll give it a read-over and might get back to you :wink:

Thanks for keeping up with all my questions and requests!