Intelligent Imaging

The linked webpage presents a collection of ImageJ macros for Intelligent Imaging (Feedback to microscope system for the secondary scan). 

An ImageJ macro able to control some microscopes (Micro-manager or Leica CAM controlled) to acquire high resolution images of only some structures (e.g. isolated cells) or events (e.g. mitosis) within a sample. The scan is sequenced as a primary (low resolution monitoring) scan and a secondary (high resolution, multi-dimensional) scan.

This macro is a plugin macro to the "Intelligent Imaging" workflow. It detects the Cytoo patterns (specific fluorsecence channel) and computes the occupancy (number of cells) of each pattern by analyzing the images of the DAPI channel. The analysis function can be easily extended to, for instance, only select the cells that are well spread on the patterns (by analyzing a third channel with a properly chosen marker of the cytoplasm).