Re: [micro-manager-general] ImageJ integration

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

Nico Stuurman @ 29/03/2020 13:45 -0300 dixit:
> Hi Carlos,
> 
> Sorry for the delay, slipped through the cracks..

No worries, thanks for you time.

> 
>> as I'm trying to get a realtime (i.e. live) graph of pinhole
>> intensities,
> 
> It would be useful to understand a bit better what your end "product"
> would be.  My guess is that you want to be able to start a live stream,
> have code that automatically finds pinholes (bright spots in the image),
> and produces data (and/or graphs) with intensities of these pinholes in
> all subsequent images.  Is that about right?

Hmm, some.
Forgive my use of terms; as I said, I'm helping others here.
They use pinhole to describe points of interest, but after reading a
lot, I guess that is not the original meaning.
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.

> 
>> I "discovered" that ImageJ seems not aware that
>> micro-manager (uM?) has a stack of images available and is only aware of
>> the displayed ones.
> 
> Correct.  You do not want to access Micro-Manager images through the
> ImageJ interface.  When we started out we very much wanted to integrate
> MM with ImageJ as much as possible, but quickly ran into all kinds of
> limitations of ImageJ (don't forget that ImageJ was never designed for
> its current use, it grew beyond Wayne Rasband's wildest imagination). 
> In the last refactoring of the MMcode, the interaction with ImageJ was
> restricted to the part where images are displayed, so ImageJ has very
> limited knowledge of the data.
> 
>> ImageJ has some tools that work on stacks or hyperstacks that do not
>> recognize uM data as such (i.e. ImageJ sees the images as 2D data).
> 
> 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.

>> I've seen many tools that bridge this gap, but all of them seem to work
>> on static data (i.e. done experiments) but I would like to use them on
>> live ones.
>>
>> Has anybody dealt with this already ? Is there a uM datastore -> ImageJ
>> hyperstack bridge of sorts ? I do not want to reinvent the wheel...
> 
> Use the MM api to access image data (i.e., see:
> https://micro-manager.org/wiki/Version_2.0_API). Once you have an MM
> Image, get an ImageJ ImageProcessor using the mm.data().ij()
> ImageJConverter
> (https://valelab4.ucsf.edu/~MM/doc-2.0.0-alpha/mmstudio/org/micromanager/data/ImageJConverter.html).
> Inserts these into an ImageJ stack anyway you want.  MM Datastores do
> not fit 1:1 to ImageJ stacks or HyperStacks, although you could write
> convenience functions if you so desire.

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.

I have been able to get the ImagePlus processor, from which I can create
a stack and dynamically add uM frames, but the only way to make ImageJ
"aware" of it seems replacing the Display image. If I do that, ImageJ
sees the stack and the tools work, but I'm breaking many assumptions by
the code, I think.

If there is no other way to have a realtime multi ROI graph of
measurements... I guess that is the way it's going to be.

> 
> Best,
> 
> 
> Nico

Thanks,
-Carlos

-- 
Carlos G Mendioroz  <tr...@ac...>