Collage of microscopy images
© Thomas Zobel

Microscopy seminars & workshops

Save the Date

Abberior STEADYCON Superresolution Workshop

We are pleased to inform you that the Münster Imaging Network together with Abberior Instruments will offer a STEADYCON Superresolution workshop and system demo at the MIC.
In preparation for the workshop, Dr. Dirk Luchtmann from Abberior Instruments will give a preparatory webinar about the STEADYCON and special requirements of sample preparation.

Preparatory Webinar
When: 26.04.2024 at 11.00 - 12.00

Zoom Link:
click to join
Meeting-ID: 618 0306 0557
Kenncode: Abberior


System Workshop & Demo
When: 10.06.2024 - 19.06.2024
Where: Multiscale Imaging Centre


Further Information:
STEADYCON Brochure
Multicolor_STED.pdf
Sample preparation tips for STED microscopy

New Seminar series
Image to Insight: Mastering Image Analysis Software Tools

Every last Tuesday of the month at 3 pm, we 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 pm
Place: Multiscale Imaging Centre, 120.223 + 120.223A, and Zoom
Zoom Link: click to join
Registration: Not required.

Date Topic Referent
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


 

| 27.06.2024 - 28.07.2024
© University of Dundee & Open Microscopy Environment

OMERO Workshop: Mastering Microscopy Data

Join us at the upcoming OMERO Research Data Management Workshop, an invaluable experience designed for PhD students, master students, researchers, lab technicians and all who are looking to streamline the organization and analysis of microscopy data. This two-day workshop will provide comprehensive training on OMERO, an open-source platform that has revolutionized the way microscopy images and data are handled.
Workshop Overview:
The session will kick off with an introduction to OMERO, highlighting its capabilities in securely managing, sharing, and viewing large bio-imaging datasets. Participants will gain insights into the core features of OMERO, including its flexible data model and intuitive user interface.

Date & Time: 27th - 28th of June, 9 am to 4 pm
Place: Multiscale Imaging Centre, 120.223 + 120.223A
Registration: Please register via mail to imaging at uni-muenster.de
20 places for participants available.

Key Takeaways:
Data Organization: Learn how to import and manage your microscopy data using OMERO’s hierarchical data structure. Understand how to tag and annotate images to enhance searchability and collaboration.
Data Visualization and Figure creation: Explore the tools within OMERO for on-the-fly visualization of images. We will demonstrate how to use OMERO’s integrated viewer to zoom, pan, and adjust the display settings of your images for better analysis. Also learn how to create publication-ready figures quickly and effortlessly using OMERO.figure.
Data Sharing and Security: Discover how OMERO supports controlled access even to very large datasets, allowing you to share all your data with collaborators.
Hands-On Training: Engage in hands-on exercises to practice importing your own data into OMERO, organizing datasets and creating figures. This practical session will equip you with the skills to leverage OMERO effectively in your own research group.

Please find more information at our wiki page: click

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!

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

Date Topic
16.03.2023 RDM4Mic
Research data management for microscopy, OMERO, data storage, analysis server
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
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
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
04.05.2023 Advanced fluorescence microscopy I
FRAP, FRET, FLIM, spectral unmixing
25.05.2023 Advanced fluorescence microscopy II
Deconvolution (Huygens), Airyscan (Zeiss), Lightning (Leica), deep learning approaches (N2V / CARE)
22.06.2023
cancelled
Super-resolution microscopy I
SIM, STED, MINFLUX, sample preparation
06.07.2023 Super-resolution microscopy
SIM, single molecule localization microscopy (SMLM, e.g. STORM, PALM, DNA-PAINT), sample preparation
  • Previous topics and dates

    Date, time and place Topics
    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

     

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.

Workshops “Image Processing”

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

Date, time and place Topics
currently no dates available  
  • Previous topics and dates

    Date, time and place 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