Re: [micro-manager-general] ImageJ integration

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

Hi Carlos,

On 3/29/2020 12:50 PM, Carlos G Mendioroz wrote:

> 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 ?

This can no be done without writing code.  Different people prefer 
different approaches to writing code.

I would:
- write a Micro-Manager plugin 
(https://micro-manager.org/wiki/Version_2.0_Plugins)
- Subscribe to the LiveModeEvent 
(https://micro-manager.org/wiki/Version_2.0_API_Events)
- When live mode starts, use the ImageJ ROIManager to query which ROIs 
are present on the image
- Get the currently displayed Image, get an ImageProcessor, calculate 
mean intensity (and other statistics of so desired)
- Push the data into a live graph created using JFreeChart.

Not trivial at all, but I have heard people asking for things like this 
for a long time. Other ways are certainly possible.


Best,

Nico