Collage of microscopy images
© Thomas Zobel

Microscopy seminars & workshops

Workshop: Basics of image analysis

The next course will be scheduled for October 2025.
Further information will be available here shortly.

Multiscale Imaging Centre, Röntgenstraße 16, Münster

Please register at imaging@uni-muenster.de giving your name and institute.

This workshop is 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. You will also learn to prepare your images for scientific figure creation.

Topics:
•    basics of image analysis (image acquisition and processing, image histogram, bit depth)
•    image enhancements
•    image segmentation
•    automated object counting
•    measurements
•    create figures (split channels, projections, scale bar, annotations)

Tools: Fiji, CellProfiler, Deep Learning Tools

Disclaimer: CiM-IMPRS students are encouraged to participate in the annual Image Analysis workshops organized by CiM-IMPRS.

More workshops coming in autumn!

  • Image segmentation using deep learning (Cellpose GUI, napari/QuPath SAM)
  • Reproducible image analysis workflows (Batch analysis using Cellprofiler and Arivis)
  • Image restoration and denoising (Huygens and other tools)
  • Research data management for microscopy (OMERO)
  • Follow us on Mattermost for the latest news and infos

Educational microscopy resources

Can’t wait for the next workshop? Start exploring microscopy with these online resources:

  • Introduction to bioimage analysis
    Highly recommended image analysis book by Pete Bankhead that covers basic concepts and Fiji, written for everyone from beginners to experienced researchers. The website offers clear explanations, practical examples, and is regularly updated with the latest techniques.
  • Beginners guide to fluorescence lifetime imaging microscopy (FLIM)
    Explore a collection of videos recorded during a symposium organised by our Imaging Network and its many partners. The playlist includes more than 20 hours of introductory lectures and interactive microscopy demonstrations.
  • Leica Science-Lab
    Online resource center provided by Leica Microsystems, featuring a diverse collection of articles, tutorials, webinars, and case studies covering advanced microscopy techniques, imaging methods, sample preparation, and image analysis across various fields such as life sciences, industrial applications, and medical specialties.
  • Zeiss Campus
    Educational platform by Carl Zeiss, offering in-depth resources on optical microscopy. It features interactive tutorials, detailed articles, and reference materials covering topics from basic microscopy principles to advanced techniques like superresolution imaging and spectral analysis.
  • Imaris by Oxford Instruments
    Official platform for Imaris, a leading software for advanced 2D, 3D, and 4D microscopy image analysis. The platform provides detailed information about Imaris’ features, AI-powered tools, modular packages, and offers educational resources, support, and a free trial.
  • MyScope – Microscopy learning environment
    MyScope is an online learning platform developed by Microscopy Australia, offering comprehensive resources on a wide range of microscopy techniques. It includes detailed learning modules as well as interactive microscope simulators. If you are new to microscopy, we highly recommend exploring the platform and trying out the corresponding simulators.

  • Past workshops & seminars

    Workshop: Basics of image analysis

    21-22 May 2025, 9:00-17:00
    16-17 June 2025, 9:00-17:00

    This workshop is 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. You will also learn to prepare your images for scientific figure creation.

    Seminar: The JupyterHub – your working environment for bioimage analysis

    13 May 2025, 15:00-16:00 (Zoom)

    The Uni Münster JupyterHub provides a comprehensive platform for image analysis with popular open-source tools like CellProfiler, Fiji, and CellPose. You will learn how to configure your server for image analysis, connect your data, and navigate the JupyterHub environment to leverage its full potential for bioimage analysis. More information about the JupyterHub (Wiki Imaging Network)

    Seminar series “Image to Insight: Mastering Image Analysis Software Tools”

    Date Topic Trainer
    26.11.2024 High-Content Data Analysis
    Tools and tricks for HC and screening data    		 Dr. Sarah Weischer
    29.10.2024 Cell and Particle Tracking
    Tracking analysis using Arivis and TrackMate    		 Dr. Sarah Weischer
    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
    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
    30.07.2024 Cellprofiler - Reproducible image analysis workflows Dr. Sarah Weischer
    25.06.2024 Advanced Image Segmentation
    Segmentation basics, Pixel Classifier, Ilastik
    Deep Learning: Cellpose, Stardist    		 Dr. Sarah Weischer
    28.05.2024 3D Visualization and Analysis using Zeiss Arivis Pro
    General overview Arivis, Visualization, 3D Analysis Pipelines, Segmentation / Arivis Hub    		 Dr. Sarah Weischer

    Workshops “Image Processing”

    Dates Topics
    11.-12.12.2024
    9:00-17:00    		 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
    27.-28.11.2024
    9:00-17:00    		 Advanced Image Analysis

    We invite all scientists from various research backgrounds to join our advanced image analysis course. This hands-on course will cover the latest techniques and tools for image processing and analysis, suitable for both beginners and experienced researchers. Bring your own image data to work on during the course, and we'll tailor the program to your needs. We will guide you through a comprehensive introduction to advanced image analysis software and tools, and provide opportunities for discussion and sharing of your own research challenges and experiences.

    Topics: overview and short introductions to advanced Fiji plugins, deep learning tools, open source software (Ilastik/Cellprofiler) as well as purchased software available at Münster University like Arivis (3D Analysis) and Huygens Professional (deconvolution & general image restoration)
    13.-14.11.2024
    9:00-17:00    		 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
    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

    Seminar series “Fluorescence microscopy”

    Dates Topics
    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

    Trainer: Jens Wendt
    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