ALMF course: Designing and performing Adaptive Feedback Microscopy experiments

Organisers: Manuel Gunkel, Lucas Schuetz, Aliaksandr Halavatyi

This online workshop is dedicated to microscope users who started or plan to perform Adaptive Feedback Microscopy experiments in a 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 how to design Adaptive Feedback Microscopy experiments for different applications.
• Test microscopes and programs available in ALMF using example applications.
• Discuss possibilities and challenges of applying feedback microscopy in participants’ projects.
• Learn about differences between an external open source pipeline involving ImageJ and AutoMic Tools and an internal pipeline integrated in the microscope software (Nikon JOBs)

Example projects:

1. Automated photoactivation of cells targeted by their phenotype
   • 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.
   • Low zoom overview
   • Identification of objects (Segmentation)
   • Second Segmentation and filtering of unwanted objects
   • High zoom imaging of individual embryos

The workshop will take place via video conference using Zoom on June 16th and 17th from 14:00 till 17:30.

Schedule:

Please register below

For questions please write to almf@embl.de

Bookings