Pipeline for automated detection of organoids, followed by imaging?


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?

Thank you

Hi Jakub,

This might be of interest to you in the short term:

In the more middle-term, I’m working on something related at the moment with a slightly friendlier GUI (I hope!) - if you’re interested, please let me know, and I can explain what we’re trying


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If you’re comfortable using Python, Micro-Magellan + pycro-manager could be used to do this. Magellan provides the GUI to set things up, Pycro-manager allows you to write short bits of code that adapt acquisition to images. Happy to give more guidance if you think this would be useful

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Thank you for the suggestions. I would like to try both approaches to see what works best (I am not very proficient with Python).
I will be in contact via email or personal messaging (as soon as my account here allows me to do so).