Use image analysis to direct image acquisition and turn your microscope in a truly automatic discovery engine.
Images acquired during the Exploration phase are analyzed by an ImageJ macro (which you will need to write yourself). When the macro finds an object of interest, Micro-Manager switches to Imaging settings and acquires data of the object of interest. Optionally, the plugin can move the object of interest to the center of the image and set a camera ROI (you will need to run the Pixel Calibrator Plugin for this to succeed). When the Imaging phase ends, the plugin will continue exploring.
You will need to define the Exploration and Imaging settings. Set up the MDA window as you desire and save the settings to a file. You will also need to provide the location of the ImageJ macro (Analysis macro). An example macro (IA.ijm is provided in the scripts directory of Micro-Manager 1.4. The script will analyze the current image and when it detects an object of interest, it should provide its X and Y coordinates through the ImageJ Results Window (use the ImageJ command Analyze particles with the Centroid measurement selected). To develop the macro, acquire a dataset at multiple locations and press the Test button of the plugin. Your macro will be run on all sites in the dataset and the objects of interest found will be displayed in a window. Clicking on a row in that window will display the corresponding object.
The Exploration Area(fields) section of the plugin lets you define the range (in rows and columns) of the exploration area. The Imaging ROI(pixels) lets you set the size of the ROI to be used in Imaging mode.
Note that the interface between this plugin and ImageJ macros may be changed in the future. Also, it will be interesting to explore integration of other programming environments. Extensions such as continuous searching of the given area (i.e. do not stop after the first round) are also possible.
–Nico 16:54, 14 October 2012 (PDT)