Collage of microscopy images
© Thomas Zobel

Microscopy seminars & workshops

New seminar series!
Image to Insight: Mastering Image Analysis Software Tools

Let's delve deeper into different image analysis software tools! Our aim is to collectively expand our knowledge, innovate with our findings, and elevate our research methods. The seminar series targets researchers who perform microscopy image analysis. Regardless of your current expertise in image analysis, this seminar series is designed to cater to all levels. Each session will carry a blend of theoretical understanding, software demonstration and open discussions.

Topics and dates

Date & time: Every last Tuesday of the Month, 3:00-4:00 pm
Place: Multiscale Imaging Centre, 120.223 + 120.223A, and Zoom
Zoom link: click to join
Registration: Not required.

Date Topic Trainer
28.05.2024 3D Visualization and Analysis using Zeiss Arivis Pro
General overview Arivis, Visualization, 3D Analysis Pipelines, Segmentation / Arivis Hub		 Dr. Sarah Weischer
25.06.2024 Advanced Image Segmentation
Segmentation basics, Pixel Classifier, Ilastik
Deep Learning: Cellpose, Stardist		 Dr. Sarah Weischer
30.07.2024 Cellprofiler - Reproducible image analysis workflows Dr. Sarah Weischer
27.08.2024 OMERO – Data Analysis of Images stored in OMERO
Import image data from OMERO into Fiji; export images and save ROIs, overlays and analysis results from ImageJ/Fiji into OMERO; Easy-to-use Python API		 Jens Wendt
24.09.2024 Image Restoration and Denoising
Basics of deconvolution and image restoration; deconvolution using Huygens, LSM+ and Thunder; deconvolution of Airyscan images; image restoration and denoising with deep learning tools		 Dr. Thomas Zobel
29.10.2024 Cell and Particle Tracking
Tracking analysis using Arivis and TrackMate		 Dr. Sarah Weischer
26.11.2024 High-Content Data Analysis
Tools and tricks for HC and screening data		 Dr. Sarah Weischer
Microscopy image
© Ali Gheisari - CMCB light microscopy facility/TU Dresden

FLIM videos on Youtube

Find a collection of videos recorded during the symposium “Beginners guide to fluorescence lifetime imaging microscopy (FLIM)”. The playlist includes more than 20 hours of introductory lectures and interactive demonstrations at the microscope. The symposium was organised by our Imaging Network together with many partners.

Seminar series “fluorescence microscopy”

We provide an introduction into different instruments and methods for fluorescence microscopy – starting with the preparation of samples as well as basic functions and instrument settings up to characteristics in the technical design of special microscopes. The techniques covered include fluorescence recovery after photobleaching (FRAP), fluorescence resonance energy transfer (FRET) and fluorescence-lifetime imaging microscopy (FLIM), super-resolution methods such as stimulated emission depletion (STED) and single molecule localization microscopy (SMLM), and single particle tracking. Everyone working at Münster University, and especially master and doctoral students, are welcome to participate!

Currently no dates scheduled.

  • Previous topics and dates

    On Thursdays, 12:00 to 13:00 p.m.
    Venue: Multiscale Imaging Centre (Auditorium), Röntgenstraße 16
    If you cannot make it in person, it's possible to join the seminar via Zoom.
    Meeting-ID: 699 7767 8482
    Code: 145159

    Speaker: Thomas Zobel, Coordinator Microscopy – Imaging Network

    Dates Topics
    06.07.2023 Super-resolution microscopy
    SIM, single molecule localization microscopy (SMLM, e.g. STORM, PALM, DNA-PAINT), sample preparation
    22.06.2023
    cancelled    		 Super-resolution microscopy I
    SIM, STED, MINFLUX, sample preparation
    25.05.2023 Advanced fluorescence microscopy II
    Deconvolution (Huygens), Airyscan (Zeiss), Lightning (Leica), deep learning approaches (N2V / CARE)
    04.05.2023 Advanced fluorescence microscopy I
    FRAP, FRET, FLIM, spectral unmixing
    27.04.2023
    cancelled    		 Basics of fluorescence microscopy II
    Confocal laser scanning microscopes, beampath, detectors (PMT, HyD, GaAsp), signal to noise ratio, tips for live cell imaging, sample preparation
    20.04.2023 Basics of fluorescence microscopy I
    Wild field systems, point spread function, numerical aperture of an objective, resolution (raylight, FWHM, Abbe diffraction limit), different kinds of fluorophores
    30.03.2023 Microscopy – what’s at hand at Münster University?
    Different microscopy systems, services (OMERO/analysis server), image analysis, provided software, examples of methods from different groups
    16.03.2023 RDM4Mic
    Research data management for microscopy, OMERO, data storage, analysis server
    19.05.2022
    12:00-13:00
    Online seminar    		 Super-resolution microscopy II
    Single molecule localization microscopy (SMLM, e.g. STORM, PALM, DNA-PAINT), single particle tracking
    12.05.2022
    12:00-13:00
    Online seminar    		 Super-resolution microscopy I
    SIM, STED, MINFLUX, sample preparation
    05.05.2022
    12:00-13:00
    Online seminar    		 Advanced fluorescence microscopy II
    Deconvolution (Huygens), Airyscan (Zeiss), Lightning (Leica), deep learning approaches (N2V / CARE)

    07.04.2022
    12:00-13:00
    Online seminar

    		 Advanced fluorescence microscopy I
    FRAP, FRET, FLIM, spectral unmixing
    24.03.2022
    12:00-13:00
    Online seminar    		 Research data management for microscopy data
    OMERO, data storage, analysis server
    17.03.2022
    12:00-13:00
    Online seminar    		 Basics of fluorescence microscopy II
    Confocal laser scanning microscopes, beampath, detectors (PMT, HyD, GaAsp), signal to noise ratio, tips for live cell imaging, sample preparation
    10.03.2022
    12:00-13:00
    Online seminar    		 Basics of fluorescence microscopy I
    Wild field systems, point spread function, numerical aperture of an objective, resolution (raylight, FWHM, Abbe diffraction limit), different kinds of fluorophores
    03.03.2022
    12:00-13:00
    Online seminar    		 Münster Imaging Network – Services & Microscopy Systems
    Overview about the services of the Imaging Network and the available microscopy systems (database & data storage, analysis server, image analysis and more)
    12.03.2021
    12:00-12:45
    Online seminar    		 RDM4Mic
    Research data management for microscopy, OMERO, data storage, analysis server
    26.02.2021
    12:00-12:45
    Online seminar    		 Super-resolution microscopy II
    Single molecule localization microscopy (SMLM, e.g. STORM, PALM, DNA-PAINT), single particle tracking
    12.02.2021
    12:00-12:45
    Online seminar    		 Super-resolution microscopy I
    SIM, STED, MINFLUX, sample preparation
    29.01.2021
    12:00-12:45
    Online seminar    		 Advanced fluorescence microscopy II
    Deconvolution (Huygens), Airyscan (Zeiss), Lightning (Leica), deep learning approaches (N2V / CARE)
    15.01.2021
    12:00-12:45
    Online seminar    		 Advanced fluorescence microscopy I
    FRAP, FRET, FLIM, spectral unmixing
    04.12.2020
    12:00-12:45
    Online seminar    		 Basics of fluorescence microscopy II
    Confocal laser scanning microscopes, beampath, detectors (PMT, HyD, GaAsp), signal to noise ratio, tips for live cell imaging, sample preparation
    06.11.2020
    12:00-12:45
    Online seminar    		 Basics of fluorescence microscopy I
    Wild field systems, point spread function, numerical aperture of an objective, resolution (raylight, FWHM, Abbe diffraction limit), different kinds of fluorophores
    23.10.2020
    12:00-12:45
    Online seminar    		 Microscopy – what’s at hand at Münster University?
    Different microscopy systems, services (OMERO/analysis server), image analysis, provided software, examples of methods from different groups

Workshops “Image Processing”

Currently no dates scheduled.

  • Previous topics and dates

    Trainer: Thomas Zobel, Coordinator Microscopy – Imaging Network

    The number of participants is limited to ten people per workshop. Please send your registration request to cim@uni-muenster.de indicating your name and institution.

    Our workshops are held online via Zoom. We work remotely on our analysis server and ideally you work with one large or two monitors. No further technical preparations are necessary in advance.

    Dates Topics
    01.-02.03.2022
    9:00-16:00
    Online workshop    		 Image processing with advanced image analysis software & tools

    Topics: overview and short introductions to advanced Fiji plugins, open source software (Ilastik/Cellprofiler) as well as purchased software available at Münster University like Imaris (3D Analysis) and Huygens Professional (deconvolution & general image restoration)

    No prerequisites for participation.
    22.-23.02.2022
    9:00-16:00
    Online workshop    		 Image processing with Fiji/ImageJ – Advanced course (macro programming)

    Topics: detailed lecture about ImageJ macro language, step-by-step programming tutorial, open to discuss and write own macros
    Important: Participation in our Fiji/ImageJ beginner course or the Biovoxxel ImageJ/Fiji course, or detailed knowledge of Fiji/first experiences with macros or other programming languages is required.
    15.-16.02.2022
    9:00-16:00
    Online workshop    		 Image processing with Fiji/ImageJ – Course for beginners

    For all scientists who work with microscopes and microscopic images! At the end of the course, you will be able to analyse your images in an automated and unbiased way and to prepare your images for scientific figure creation.

    Topics: basic image acquisition and image processing, image histogram and bit depth, image enhancements (background subtraction/using filters for further analysis), image segmentation (e.g. counts of nuclei, creation of regions of interest), (ROI) etc., automated object counting, measurements (e.g. signal quantifications), create figures (split channels, projections, scale bar, annotations), macro recorder and batch processing
    08.-09.02.2022
    9:00-16:00
    Online workshop

    Image processing with Fiji/ImageJ – Course for beginners

    For all scientists who work with microscopes and microscopic images! At the end of the course, you will be able to analyse your images in an automated and unbiased way and to prepare your images for scientific figure creation.

    Topics: basic image acquisition and image processing, image histogram and bit depth, image enhancements (background subtraction/using filters for further analysis), image segmentation (e.g. counts of nuclei, creation of regions of interest), (ROI) etc., automated object counting, measurements (e.g. signal quantifications), create figures (split channels, projections, scale bar, annotations), macro recorder and batch processing