Re: [micro-manager-general] ImageJ integration

[Carlos G M. <tr...@ac...>]

Hey Nico,

Nico Stuurman @ 29/03/2020 16:35 -0300 dixit:
> 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.

Hmm, let's define my understanding:
Image: 2D (XY)
Stack (ImageJ): series of images (3D) where the third dimension could be
Z, c or t.
Hyperstack: 4 or 5 dimension data.

So as far as I get, for ImageJ, a stack is just a series of images along
some axis (Z, c, t). If this is not so, I'm sure confusing you. Sorry.

>>> 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.

I don't want to stay anywhere :) I just want a usable option.
Are you saying that there is a way for stock Micro-Manager to make a
realtime t-axis graph of ROI intensities ? Great! Care to point me how
to do that ?

> 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).

I'm open to do it in the best way you see fit, given that you sure have
a better grasp of what could be useful even for the community.

> 
>> 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.

Well, at least we are in synch: ImageJ is not aware of more than 2
dimensions. Thus any transversal analysis has to be done outside ImageJ.

> 
> Best,
> 
> 
> Nico
-- 
Carlos G Mendioroz  <tr...@ac...>