I have a question regarding setting up an automated image acquisition pipeline for a micro-manager controlled microscope.
Setup: Nikon TE2000 body with micro-manager controlled Marzhauser XYZ stage and Thorlabs camera
Image acquisition aims: to automate the detection and acquisition of low magnification images of fluorescently tagged organoids in a 24-well plates.
To explain, would it be possible to setup a macro for micro-manger to first scan entire area of each well of a 24-well plate and upon detection of a strong fluorescent signal by the camera (membrane labelled organoid) take several predetermined size images in XY and Z within that region. Those images will then later be inspected separately, stitched in XY and used for organoid characterisation.
Any hints or suggestions on how to proceed with this would be very much appreciated. I am quite familiar with ImageJ macros but I have not worked with Micro-manager much.
Perhaps there are already macros available that I can use as a basis for this?