Re: [micro-manager-general] ImageJ integration

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

Nico Stuurman @ 30/03/2020 16:01 -0300 dixit:
> 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.
> 
> 

Ok, at least I was not very confused :)
I will have to digest the plugin API, I don't mind sharing back the code
when it is done. Too bad we can not use simmilar functions that are
already there.

Given that I've found a loophole that seems to work (tricking ImageJ
into thinking that it has a stack) it might take time, but who knows ?

> Best,
> 
> Nico

Thanks again,
-Carlos

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