COMMERCIAL RESPONSE (since I work for ZEISS)
Hi Thomas,
when you mean a workflow like
1) Acquire Overview Images
2) Analyze for "Interesting Structures" using the microscope software or Fiji/ImageJ (or something else)
3) Import the results to the microscope SW and
4) perform a detailed scan using the acquisition SW
you might want to try out ZEN Blue and its Open Application Development Module. ZEN Blue also is capable of doing Online Image Analysis in order to modify the running experiment or drive the hardware (Experiment Feedback).
But the best solution (like always) depends what you real application is. You can also give Micromanager & MATLAB a try ...
Cheers,
Sebastian
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