Re: [micro-manager-general] ImageJ integration

[Nico S. <nic...@uc...>]

Hi Carlos,

On 3/29/2020 10:42 AM, Carlos G Mendioroz wrote:
> So the use case is realtime multiple ROI intensity tracking.
> The ROIs will me manually setup on a live stream, and then they want to
> have a multi plot of corresponging intensities, updating as the
> aquisition goes. They want to use that as feedback for changing some
> experiment variables.

Is this a live stream of a single channel or multiple channels? Asking 
because you seem to really want a stack and I don't understand why.  
Also, I am pretty sure that others have developed similar plugins, 
although none were ever contributed back to Micro-Manager.

>> What tools do you want to use that work on stacks?
> There you have ROI manager, multiple ROI measurements, plots (even
> "live" that e.g. change as you change a line of interest). And ImageJ
> native plugins.

ROI manager works fine within Micro-Manager, even the ImageJ live Plot 
Profile works in Micro-Manager  live mode, so if you want to stay 
completely on the ImageJ side of things, I would look at that code and 
modify to your purpose.

However, if I would work on this myself, I would build a Micro-Manager 
plugin that uses the MM api.  The advantage is that it will work with 
"live" multi-channel images and could be extended to do things like live 
ratio-tracing of multiple ROIs (useful for calcium imaging and similar 
applications).

> The issue that I find is that the ImageJ GUI is not aware of the stack,
> or at least I have not been able to do it in a proper way.

In live imaging, be it ImageJ or MM, there is no stack, there is the 
current image that is continuously being replaced by the next one. You 
want to measure each image, store those measurements, and possibly 
display them live while the acquisition is ongoing.

Best,


Nico