ALMF course: Design and operation of Adaptive Feedback Microscopy experiments

almf   2023-04-25   Comments Off on ALMF course: Design and operation of Adaptive Feedback Microscopy experiments

Date(s) - 2023-04-25
10:00 CEST - 18:00 CEST

ALMF course: Designing and performing Adaptive Feedback Microscopy experiments

Organisers: Aliaksandr Halavatyi, Manuel Gunkel

This workshop is dedicated to microscope users who started or plan to perform Adaptive Feedback Microscopy experiments in the near future. Even though the hardware communication interfaces are different depending on the microscope brand, the principles underlying automated acquisition pipelines are often very similar. During the workshop we will use the confocal microscopes available in ALMF in combination with commercial and open-source software solutions for Feedback Microscopy to learn and test the power and flexibility of Adaptive Feedback Microscopy methodology.

Aims of the workshop:

  • Learn about capabilities of adaptive feedback microscopy methodology.

  • Learn how to design feedback microscopy experiments for different applications.

  • Set up and test image analysis and feedback decisions generating procedures using AutoMicTools – an open-source set of FIJI plugins solution developed and maintained in ALMF.

  • Test microscopes available in ALMF using example applications using either feedback microscopy procedures in-built into the microscope software or AutoMicTools pipelines.

  • Discuss possibilities and challenges of applying feedback microscopy in participants’ projects.

Example projects:

  1. Automated photoactivation of cells targeted by their phenotype. (Practical 1)
    • Low zoom overview

    • Automated Identification of cells (Segmentation)

    • Selecting cells with the particular phenotype

    • Photoactivation of selected cells

  2. Finding, sorting (size and color) and imaging of fly embryos. (Practical 2)
    • Low zoom overview

    • Identification of objects (Segmentation)

    • Second Segmentation and filtering of unwanted objects

    • High zoom imaging of individual embryos

The workshop will take in the ALMF on April 25th from 10:00 till 18:00.


Estimated Time Topic
10:00 – 11:00 Lecture: introduction to feedback microscopy (open for everyone at EMBL via Zoom)
11:00 – 12:00 Practical: use of AutoMicTools for testing image analysis and decision making in feedback microscopy
12:00 – 13:30 Lunch break
13:30 – 15:30 Practicals 1 + 2
15:30 – 16:00 Coffe break
16:00 – 18:00 Practicals 1 + 2 (swapped groups)

Zoom link for lecture:
Meeting ID: 978 9613 2519
Passcode: 977531

Please register below

For questions please write to


This event is fully booked.