Collage aus Mikroskopiebildern
© Thomas Zobel

Mikroskopie Seminare & Workshops

Workshop: Grundlagen der Bildanalyse

27.-29. Oktober 2025, 9:00-13:00
Multiscale Imaging Centre, Röntgenstraße 16, Münster

Bitte melden Sie sich unter Angabe Ihres Namens, Instituts und des Workshop Titels unter imaging@uni-muenster.de an.

Dieser Workshop richtet sich an alle Wissenschaftler:innen, die mit Mikroskopen und mikroskopischen Bildern arbeiten. Am Ende des Kurses werden Sie in der Lage sein, Ihre Bilder auf automatisierte und unvoreingenommene Weise zu analysieren. Sie werden außerdem lernen, Ihre Bilder für die Erstellung wissenschaftlicher Abbildungen vorzubereiten.

Themen:
•   Grundlagen der Bildanalyse (Bildaufnahme und -verarbeitung, Bildhistogramm, bit-Tiefe)
•   Bildverbesserungen
•   Bildsegmentierung
•   Messungen
•   Erstellen von Abbildungen (geteilte Kanäle, Projektionen, Maßstabsbalken, Anmerkungen)

Tools: Fiji, Deep Learning Tools

Hinweis: CiM-IMPRS-Studierende werden gebeten, an den jährlichen CiM-IMPRS-organisierten Bildanalyse-Workshops teilzunehmen.

Workshop: Reproduzierbare Bildanalyse von Morphologie und Dynamik

Der nächste Kurs ist für Ende des Jahres geplant.
Multiscale Imaging Centre, Röntgenstraße 16, Münster

Interesse? Dann schreiben Sie uns gern, welche Themen Sie besonders interessieren: imaging@uni-muenster.de. Auf Basis Ihrer Rückmeldungen werden wir Format und Inhalte des Workshops finalisieren. Eine aktualisierte Workshop-Agenda wird rechtzeitig hier veröffentlicht. Wir freuen uns auf Ihre Rückmeldungen!

Der Workshop vermittelt zentrale Methoden der reproduzierbaren Bildanalyse in der Mikroskopie. Zu den Themenschwerpunkten gehören Bildrestauration, Segmentierung, 3D-Analyse und Tracking – alle innerhalb strukturierter Workflows.

Tools:
•   Huygens: Dekonvolution und Bildrestauration
•   CellPose: Segmentierung von Objekten mittels Machine Learning
•   Arivis: 3D-Visualisierung, räumliche Analyse und Tracking
•   CellProfiler: Automatisierte, reproduzierbare Bildanalyse-Workflows
•   TrackMate: Zell- und Partikel-Tracking

Workshop: Forschungsdatenmanagement in der Mikroskopie

25. November 2025, 9:00-17:00
Multiscale Imaging Centre, Röntgenstraße 16, Münster

Bitte melden Sie sich unter Angabe Ihres Namens, Instituts und des Workshop Titels unter imaging@uni-muenster.de an.

Dieser praxisorientierte Workshop richtet sich an Wissenschaftler:innen, die ihre Kompetenzen im Bereich Forschungsdatenmanagement (FDM) ausbauen möchten. Durch gutes Datenmanagement werden Bilddaten auffindbar, zugänglich, interoperabel und wiederverwendbar – ganz im Sinne der FAIR-Prinzipien.

Themen:
•    Einführung in die Grundlagen des Forschungsdatenmanagements (mit Fokus auf Mikroskopiedaten)
•    Best Practices zur Datenorganisation & Dokumentation 
•    FAIR-Prinzipien und warum wir OMERO dafür empfehlen
•    Hands-on: Erste Schritte mit OMERO – Upload, Annotation und Verwaltung von Bilddaten
•    Was, wie und warum annotieren? Einführung in REMBI und Ontologie-basierte Metadaten mit OMERO

 

Selbstlernangebote zur Mikroskopie

Bis zum nächsten Workshop dauert es noch zu lange? Dann entdecken Sie Mikroskopie mit diesen Online-Ressourcen:

  • Einführung zur Bioimage-Analyse [en]
    Sehr empfehlenswertes Buch zur Bildanalyse von Pete Bankhead, das grundlegende Konzepte sowie Fiji behandelt, geeignet für Einsteiger:innen bis hin zu erfahrenen Forschenden. Die Website bietet klare Erklärungen, praktische Beispiele und wird regelmäßig mit den neuesten Techniken aktualisiert.
  • Einsteigerleitfaden zu Fluorescence Lifetime Imaging Mikroskopie (FLIM) [en]
    Eine Sammlung von Videos, aufgenommen während eines Symposiums das von Münster Imaging Network und vielen Partnern organisiert wurde. Die Playlist umfasst über 20 Stunden Einführungsvorträge und interaktive Mikroskopie-Demonstrationen.
  • Leica Science-Lab [en]
    Online-Ressourcenzentrum von Leica Microsystems mit einer vielfältigen Sammlung an Artikeln, Tutorials, Webinaren und Fallstudien. Thematisiert werden fortgeschrittene Mikroskopietechniken, Bildgebungsverfahren, Probenvorbereitung und Bildanalyse in Bereichen wie Lebenswissenschaften, Industrie und Medizin.
  • Zeiss Campus [en]
    Bildungsplattform von Carl Zeiss mit umfangreichen Inhalten zur optischen Mikroskopie. Enthält interaktive Tutorials, detaillierte Artikel und Referenzmaterialien, von Grundlagen der Mikroskopie bis hin zu fortgeschrittenen Techniken wie Superresolution Imaging und Spektralanalyse.
  • Imaris von Oxford Instruments [en]
    Offizielle Plattform für Imaris, eine führende Software zur 2D-, 3D- und 4D-Bildanalyse in der Mikroskopie. Die Website bietet umfassende Informationen zu Funktionen, KI-gestützten Tools, modularen Erweiterungen sowie Lernmaterialien, Support und eine kostenlose Testversion.
  • MyScope – Lernplattform für Mikroskopie [en]
    MyScope ist eine Online-Lernplattform von Microscopy Australia mit umfassenden Inhalten zu verschiedensten Mikroskopietechniken. Sie enthält detaillierte Lernmodule sowie interaktive Mikroskopsimulatoren. Besonders für Mikroskopie-Neulinge ist ein Besuch der Plattform und das Ausprobieren der Simulatoren sehr zu empfehlen.

  • Vergangene Workshops & Seminare

    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