Imaging Network – Microscopy

  • News

    Register Now:
    Beginners Guide to Fluorescence Lifetime Imaging (FLIM) in Life Sciences

    We are happy to announce an online symposium about fluorescence lifetime imaging (FLIM) that will provide the opportunity for life scientists to learn and explore the applications of FLIM in their research.

    When: 23-27 November 2020
    Where: Virtually everywhere

    The symposium will cover the wide spectrum of the techniques, methods, and applications of FLIM, particularly tailored to be a bench-side how-to manual. Over the course of a week, participants will learn the principles of FLIM, the key issues in the field of data acquisition and analysis, and what approaches are available for applying in their research. The hands-on sessions are specially planned to provide the tutorials for everyone regardless how new or experienced they might be in the field.

    The overall goal of the symposium is to provide the life scientists with practical knowledge ready to apply in their daily work. It will also serve as an opportunity for FLIM experts to get to know each other, share expertise, and establish collaborations. We see it as a nonconventional learning opportunity for everyone.

    We encourage everyone interested in FLIM, students, postdocs, scientific staff, and group leaders, to register and attend the virtual symposium. For more information and registration please check the symposium webpage.
    Register here [en]

    Organized by:
    Ali Gheisari (TU Dresden), Thomas Zobel (WWU Münster), Stefanie Weidtkamp-Peters (HHU Düsseldorf), Steffen Dietzel (LMU München), and Mariano Gonzalez Pisfil (LMU München)

    DeepLearning based denoising with Noise2Void

    N2V denoising on an CLSM Image

    Click on the image to open it with OMERO.iviewer

    Noise2Void can be used for denoising your images without the need for a ground truth. Training can be done on single noisy images in Fiji. Noise2Void can also be used if deconvolution is not possible due to unsuitable imaging parameters. Furthermore it can be used for almost all kinds of images, like EM, RGB, photographs etc. Curious what it can do for your images? You are welcome to contact me @Mattermost or by mail.

    Read the paper: Noise2Void - Learning Denoising from Single Noisy Images | Noise2Void on Github

    Super-resolution microscopy with DNA-PAINT


    Reconstruction of a DNA-PAINT imaging sequence. 20nm DNA origami nanorulers are shown in red. The original pixelsize during detection is shown in green.

    In March 2020 I attend the Trends in Microscopy (TiM-2020) summer school, an awesome event with microscopy hands on sessions from 9am - 12pm! We also did DNA-PAINT experiments with around 4nm resolution in an crowded and warm microscopy room. The technique is rel. simple to use and we have a group with quite a lot of experience with it. Just contact me if you are interested.
    Thomas Zobel

    Original Paper: Super-resolution microscopy with DNA-PAINT Joerg Schnitzbauer, Maximilian T Strauss, Thomas Schlichthaerle, Florian Schueder & Ralf Jungmann Nature Protocols volume 12, pages1198–1228(2017)


    Data management for microscopy

    OMERO stands for Open Microscopy Environment Remote Objects and is a client server environment. From the microscope to publication, OMERO handles all your images in a secure central repository which is designed for long term storage. You can view, organize, analyze and share your data from anywhere you have internet access. Work with your images from a desktop app (Windows, Mac or Linux), from the web or from 3rd party software. Over 140 image file formats supported, including all major microscope formats. The usage of OMERO as a data starage for your aquisition data is free of charge.

    With OMERO.figure we provide a tool for easy and rapid figure creation. Each panel of the figure becomes a multi dimensional image viewer, allowing you to zoom and pan, adjust rendering settings and even scroll through Z and Time. Figures can be exported as TIFF images or PDF documents, so you can move seamlessly to other editing tools such as Adobe Illustrator.

  • Huygens DCV

    Huygens – deconvolution and image restoration

    The Imaging Network offers two network licenses for the use of Huygens Professional. Huygens can be used to process almost all types of microscopic images. Resolutions of up to 120nm can be achieved even on a standard confocal microscope. Also widefield and spinning disc images can be significantly improved in their resolution and signal-to-noise ratio.

    Official website Huygens

    Nyquist Calculator
    The Nyquist Calculator calculates the optimal settings (pixel sizes and z-steps) for images intended for deconvolution. Also available as App.

    Brief introductions Huygens

  • Fiji

    Official website Fiji
    Fiji is an image processing package – a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. Forum
    Microscopy community forum

  • Misc

    Open source software

    • PSFj
      A tool to probe your microscope's performance
    • LAMA – LocAlization Microscopy Analyzer
      A tool that extracts quantitative information from single-molecule super-resolution imaging data
    • rapidSTORM
      Evaluation tool that provides fast and highly configurable data processing for single-molecule localization microscopy

    Manufacture sites with reviews, webinars and technique explanations

    Spectra viewer

  • Training

    If you need an introduction to a specific system, please contact the responsible person of the system or a member of our team. Short courses for small groups (e.g. about basic confocal imaging or super-resolution techniques etc.) can be given by our team after prior consultation.

  • Support

    If you have any questions, you can contact us at any time by e-mail. If you have questions on a specific topic, you are also welcome to use our internal university support channels at Mattermost:
    Mattermost support channels:  OMERO | Booking Schedule | Imaging Techniques | Events