Re: [micro-manager-general] ImageJ integration

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

Hi Carlos,

On 3/30/2020 12:34 PM, Carlos G Mendioroz wrote:
> Nico Stuurman @ 30/03/2020 16:01 -0300 dixit:
>> I would:
>> - write a Micro-Manager plugin
>> (https://urldefense.proofpoint.com/v2/url?u=https-3A__micro-2Dmanager.org_wiki_Version-5F2.0-5FPlugins&d=DwICaQ&c=iORugZls2LlYyCAZRB3XLg&r=UwP8SWqih8VHO1LwZpgcx83I4o21yLj6V6QD-25Dt4I&m=VRIJ8_KFVROqTyxIGcwMQ3sbaB3Ad8fh2YoxAHVpBvA&s=7bkv8yedZWX9BjvrRKXeNSyUGPuC4Siku1bU44e5Ouk&e= )
>> - Subscribe to the LiveModeEvent
>> (https://urldefense.proofpoint.com/v2/url?u=https-3A__micro-2Dmanager.org_wiki_Version-5F2.0-5FAPI-5FEvents&d=DwICaQ&c=iORugZls2LlYyCAZRB3XLg&r=UwP8SWqih8VHO1LwZpgcx83I4o21yLj6V6QD-25Dt4I&m=VRIJ8_KFVROqTyxIGcwMQ3sbaB3Ad8fh2YoxAHVpBvA&s=LFEo4OxYlyFhO9uqAKbEyhJyjGgnkGRVsF7hE1DfgUg&e= )
>> - 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.
> do live mode events get generated by MDA ?

No, live mode events are generated when the user starts live mode. I 
thought the goal of the project was to track intensities of of ROIs 
during live mode?  If you just want to do this at the end of an MDA, 
then thing are much easier.

> Do you have a template plugin suggestion that I can use as a starting
> point ?

The example plugin 
(https://github.com/micro-manager/micro-manager/tree/master/plugins/Example/src/main/java/org/micromanager/plugins/example) 
is a good place to start. You may also want to look at the Tracker 
plugin 
(https://github.com/micro-manager/micro-manager/tree/master/plugins/Tracker/src/main/java/com/imaging100x/tracker), 
as it tries to do stuff with live data.

Best,


Nico