Our Service: We support you in all aspects of microscopy – from experimental design to publication. Here you’ll find an overview of the assistance we offer for planning experiments, managing, and analysing microscopy data. You will also find information on how we help you with publication.
Further services:
For planning and documenting experiments, we strongly recommend using the electronic laboratory notebook. This service is provided by the University Library Münster (ULB) to all members of the University of Münster and based on the software eLabFTW.
We recommend the OMERO platform (Open Microscopy Environment Remote Objects) to anyone who wants to take a structured approach to Research Data Management (RDM). OMERO was specifically developed to organise microscopy data in a sustainable, traceable, and collaborative way. Large image datasets can be stored centrally, securely, and for the long term, linked with metadata, and made accessible across projects. OMERO is available as a desktop application (Windows, Mac, or Linux), via the web, or through third-party software, and supports over 140 image file formats. The Münster Imaging Network provides OMERO and actively supports you in the implementation and customisation of your workflows.
Numerous plugins extend OMERO with practical features. Particularly noteworthy is OMERO.figure, which allows annotated figures for publications to be created directly within OMERO. Each panel of the figure in OMERO.figure is multidimensional and allows zooming, panning, and scrolling through Z-planes and time points. Figures can be exported as TIFF images or PDF documents, enabling seamless transition to other editing tools such as Adobe Illustrator.
Downloads OMERO Insight client
Links and support
Further OMERO plugins and tools can be found in our toolbox (see below).
The analysis of microscopy data makes it possible to extract quantifiable information from images. Modern software supports efficient, reproducible, and scalable evaluation. To process large volumes of data and to utilise automated or interactive analysis workflows, a powerful infrastructure, such as server solutions and web-based analysis environments, is essential.
Fiji – interactive und handy analysis
Fiji is an ImageJ distribution that provides a comprehensive collection of plugins and scripting support for efficient processing and analysis of biological microscopy data.
Official website Fiji
CellProfiler – analysis of large datasets
CellProfiler automates the analysis of large amounts of biological image data using batch processing and pipeline workflows, for example for cell counting or structure detection.
Official website CellProfiler
Arivis Pro – 3D visualization and analysis
Arivis Pro is optimised for confocal and light-sheet microscopy and visualises large 3D and 4D microscopy datasets with advanced rendering, segmentation, and quantification workflows.
ZEISS Arivis Pro (accessible from the university network)
Further tools, AI support, and infrastructure can be found in our Toolbox (see below).
Ready for publication? We support making research accessible in a simple, meaningful, and FAIR way. We take care of your microscopy data so you can focus on your research:
We also provide guidance with publishing datasets in public repositories such as the Image Data Resource (IDR), the BioImage Archive (BIA), or our local OMERO instance. Feel free to contact our team at any time!
FAIR stands for:
The goal is to use research data in a sustainable, efficient, and transparent way.
This is a comprehensive overview of the tools we regularly use and recommend as part of our microscopy workflows. If you have any questions, feel free to reach out — we’re also happy to test and consider new tools.
Arivis Hub
Central access point for projects, models, and workflows in the Arivis ecosystem, with support for batch analysis and execution of pre-defined analysis pipelines.
Arivis Pro
Visualises and analyses large 3D and 4D image datasets, e.g., from confocal or light sheet microscopy.
CellProfiler
Automates the analysis of large amounts of biological image data, for example for cell counting or structure detection, using batch processing and pipeline workflows.
Huygens Professional
Specialized in deconvolution of microscopy images to improve image quality. Corrects blurring and optical distortions caused by the microscope system. Compatible with various microscopes. The Münster Imaging Network offers two network licenses for using Huygens Professional.
Official Huygens website
Huygens quick guide
NyquistCalculator
The Nyquist Calculator determines optimal settings (pixel size and Z-step size) for image acquisition intended for deconvolution. Also available as an app.
Fiji
Image analysis software with many plugins for processing and analysing biological microscopy images.
LAMA – LocAlisation Microscopy Analyser
Extracts quantitative information from single-molecule localisation data, e.g., for SMLM analysis.
Picasso (for DNA-PAINT Analysis)
Analysis and reconstruction software for high-resolution DNA-PAINT data.
PSFj
Tool for evaluating microscope performance by analysing the point spread function (PSF).
QuPath
Enables visual annotation and quantitative analysis in digital pathology, e.g., slidescans of tissue sections.
rapidSTORM
Fast and highly configurable processing tool for single-molecule localisation microscopy (SMLM) data.
rapidSTORM
Arivis Cloud (Train your AI-Segmentation)
Online training platform for creating custom segmentation models.
Cellpose
AI-based tool for automatic cell segmentation in microscopy images.
Cellpose GUI
User-friendly interface for Cellpose to manually control, review, and further improve segmentations by refining the model through targeted retraining.
CSB-Deep (CARE, Noise2Void)
AI models for image restoration (e.g., denoising) without the need for ground truth.
Ilastik
Pixelclassifier enabling machine learning without programming skills for segmentation, classification, and tracking.
Napari
Our reccomondation for the latest AI-tools: A fast, interactive viewer for multidimensional microscopy images with plugin extensions based on Python.
SAM/µ-SAM
AI models for general (or microscopy-specific) segmentation of arbitrary image contents via interactive selection.
StarDist
Deep-learning-based tool for precise segmentation of round or elliptical structures such as cell nuclei, even when they strongly overlap.
Hive analysis server
Central high-performance computing resource for image analysis workflows and software usage.
Hive (Wiki- accessible from the university network)
JupyterHub BioImage analysis
Browser-based platform for image analysis with pre-installed tools.
JupyterHub (Wiki- accessible from the university network)
Uni-Cloud (Compute & Storage)
Cloud-based environment for storing and processing scientific image data.
eLabFTW
Electronic lab notebook for documenting and sharing experiments and metadata within the research team.
Leo/Adamant
Tools for structured metadata collection and data description following FAIR principles.
OMERO
Central database for structured storage, organisation, and sharing of microscopy image data.
OMERO - CellProfiler Batch Notebook
Combines OMERO data management with CellProfiler analysis in Jupyter Notebooks and enables automatic reupload of analysis results.
OMERO - Fiji Plugin OMERO_batch
Automates the image analysis of entire data sets with Fiji directly from OMERO.
Insight Plugin for ImageJ / Fiji
OMERO.figure
Creates annotated figures for publications directly from OMERO.
OMERO.OpenLink
Generates publicly shareable links to OMERO images.
OMERO.OpenLink (Wiki – accessible from the university network)
OMERO - Tag Search
Modern search engine for user-defined tags (keywords) in OMERO.
RDM-Desktop
Tool to support best practices in research data management.
Scripts (Key-Value from csv / Labeled Images etc.)
Small automation scripts for tasks such as image labeling or metadata transfer.
Tabbles
Helps organise and tag files regardless of storage location.
Templates (csv, yaml, json)
Templates for standardised documentation and further processing of metadata.