PreSemester MICROSCOPY Course 2022/2023

September 26, 2022 @ 10:00 – October 6, 2022 @ 11:30
ISTA campus
Am Campus 1

PreSemester MICROSCOPY Course 2022/2023

The (pre-semester) microscopy course is organized by the Imaging & Optics Facility (IOF) and aims to generate the understanding of how to design your experiments using matching imaging techniques. As a red line we raise awareness of the importance of proper data acquisition and the timely image analysis assessments during essay establishment: timely assay-evaluation is critical to determine if the fundamental ‘properties of process of interest’ can be resolved and quantified by the used imaging approach. To this aim, participants will be introduced to contemporary microscopy techniques, with a focus on the methods that are available at ISTA campus. Lectures will cover microscopy-related principles of optics, principles of fluorescence, anatomy of the microscope, sample preparation, methods of optical sectioning, image acquisition methods, super-resolution technologies, basics of electron microscopy and the basics of data analysis.

the Imaging &Optics Facility is providing the ‘Annual Microscopy Course’ on 26- 27 September (all day), and on 3-6 October (half day mornings).

Details for registration for the course will be made available on the new  ISTA Graduate-School Athena Platform:

The Microscopy Course uses the online Moodle PlatformC_OTH-301_F22).


  • ‘Students’  join for 2 ECTS credits and will have manditory participation in all lectures, on-system demonstrations (100% attendance required) and require to complete an exam at the end of the course (max 12 students)
  • ‘Audit Students’ can join lectures and we will fill up vacant hands-on spots by order of registration (Zoom links will be shared to registered participants)

We will place links to lecture slides, hand-outs for hands-on as well as links to sample data for the image analysis sessions on the course overview below. Links provided will be to an internal ‘ Seafile’ location for which one needs to be within the IST network (on campus / VPN).

The zoom links are embedded in times.

Course Overview and Materials

Monday, September 26, 2022

– Tuesday, September 27, 2022


– Monday, October 3, 2022 – Sunstone Building

– Tuesday, October 4, 2022 – Sunstone Building

– Wednesday 5, October 5, 2022 – Lab West Heinzel Room

  • (09:00-10:00h) Lecture 5.1: What is a digital image? (Slides)
  • (10:15-11:15h) Demonstration: 5.2: ImageJ / FIJI: image analysis (Slides)
  • (11:30-12:30h) Lecture 5.3: Machine Learning in Image Analysis (Slides)

– Thursday, October 6, 2022




Your Imaging & Optics Facility team