The Core Facility

The Image Analysis Core Facility (IACF) runs open and remote services in image analysis to support life scientists and medical researchers visualize, analyze, and extract quantitative information out of their bioimaging datasets from anywhere.

Our team of experts is here to discuss your image analysis needs, guide and train you in the most suitable software solutions, and if needed develop a complete image analysis workflow tailored to your scientific project. We leverage an extensive hardware and software infrastructure designed for remote image analysis, including a pool of latest-generation workstations, innovative High Performance Computing and data exchange services, and a broad range of bioimage analysis software tools.

The facility actively promotes open science and the most efficient data sharing with the scientific community according to the FAIR principles. We are collaborating with the Danish e-Infrastructure Collaboration (DeiC), the Network of European BioImage Analysts (NEUBIAS) and Euro-BioImaging, and we are engaged in multiple training and dissemination activities.

Image Analysis

  • If you have some concrete image analysis needs, please fill in our Project Application form and we will do our best to quickly process your request and get back to you (typically within 10 days).

  • If you are not entirely sure if your images are suitable for quantitative analysis, or if you struggle to define your image analysis problem, please register to our free bi-monthly Call4Help consultation to discuss it.

  • If you are using a bioimage analysis software that we support at the facility and want to brush up your knowledge or go a notch further, you can inquire about software training.

The success of scientific image analysis depends on multiple factors, it is hence important to initiate the conversation with us early in your project, ideally just after acquiring the first representative images. Furthermore, the quality of the images acquired is key and we recommend seeking guidance from your local bioimaging facility to get an imaging specialist involved in the conversation!

Please read our Terms of Service and Rates before contacting us !

The code repositories associated to these projects will be shared publicly upon publication. Feel free to contact us before if you have an urgent need.

  • Estimation of Myonuclear domains from the assisted segmentation of muscle fiber nuclei (Imaris + Matlab)

    Collaboration with Christian Høgsbjerg and Abigail Mackey (Bispebjerg Hospital / University of Copenhagen)

  • 3D segmentation and morphological analysis of mitochondria from confocal images (ImageJ)

    Collaboration with Jette Bach Agergaard (University of Copenhagen)

  • Identification of sister chromatid exchanges from metaphase chromosome spreads (ImageJ)

    Collaboration with Michael Lisby and Park Sohyun (University of Copenhagen)

  • Classification of centralized nuclei from muscle fibers (QuPath)

    Collaboration with Zhenzhen Wu (University of Copenhagen)

  • Scope

    • IACF will not extract and interpret scientific results on behalf of researchers but will train and support researchers in using software tools specifically customized to analyze their data.

    • Training and support will be provided by our staff exclusively on our workstations. We will generally not provide support for the installation of software tools on external workstations.

    Acknowledgments and intellectual property

    • IACF remains the owner of the software tools developed, and will seek the consent to share these assets publicly.

    • IACF commits not to disclose any material provided by the user (including Images, research data and results) to any third party without prior written consent.

    • IACF should be acknowledged in publications reporting results derived from IACF services (including access to workstations and training on existing tools), minimally with the following sentence: "We acknowledge the Danish Bioimaging Infrastructure Image Analysis Core Facility for the support in the image analysis work presented”.

    • For publications involving a novel image technique or an image analysis tool specifically developed by IACF, the contributing staff should be co-author and supervise the description of that method.

    Shared Storage

    • The shared storage provided by IACF is, unless specific measures are taken, accessible by any user of the facility.

    • IACF cannot be held responsible for data loss, you should always keep a backup in your own storage.

    • Please use the shared storage responsibly, and erase your files promptly after processing. Any non traceable data, or data not accessed for over 3 months will be deleted (after notice for the last).

    • Please contact us if your total storage needs is expected to exceed 1 TB.

    For more details, Please refer to the complete Terms of Service and Protocol document.

  • Windows Workstations: 150 Kr/h

    Personal Training/Support: 500 Kr/h

    Software development: 750 Kr/h

    Indicative costs for sample projects

    • One-to-one QuPath Training (2h): 1.000 Kr

    • ImageJ script Custom Development (4h Dev. + 1h Training): 3.500 Kr

    • Deep Learning workflow setup and tuning (16h Dev. + 2h training): 10.000 Kr

    • Multi-Component IA Workflow Development (40h Dev. + 4h Training): 25.000 Kr

    Special regimes and discounts

    • According to Danish Competition Law, Commercial Users are charged double Rates.

    • We offer a 50% discount on the booking of Windows workstations from 18:00 to 8:00 or during weekends.

    • IACF offers free software development quotation and discounts for projects >10h (see indicative costs above).

  • We maintain a pool of Windows workstations running a software stack compatible with our image analysis tools and workflows. These workstations bring last generation hardware optimized for image analysis and deep learning.

    This is the solution of choice for interactive image analysis and visualization.

    DBI Workstations (3x available)

    • AMD Ryzen 9 7950X (16 cores, 5.7 GHz)

    • Kingston FURY Beast 128GB RAM (4800 MT/s)

    • NVIDIA GeForce RTX 4090 (24 GB GDDR6X)

    • Kingston KC3000 4 TB NVMe PCIe Gen 4 (Swap Drive)

    • Seagate Exos X20 20 TB HDD (Local Data Drive)

    The workstations can be booked both for in-person and remote access (KU-VPN).

  • Linux HPC-powered remote environments (UCloud) can be used to run our image analysis tools and workflows through interactive remote desktop (VDI) or headless batch processing. This environments are fully private and GDPR compliant.

    This is the solution of choice for long headless CPU intensive jobs running on open source software.

    Note: Only available through DeiC WAYF to researchers affiliated to a Danish institution.

  • The following services can be used to upload image datasets to our computing environments:

    • ERDA: HTTP File server to share sample datasets with IACF on project submission (Public access)

    • Webfile: HTTP File server to IACF shared storage drive (requires KU user, suitable for transfer <10 GB)

    • SFTP: Secured FTP to IACF shared storage drive (requires KU user, suitable for large file transfer)

    • DeiC UCloud: Provides services to upload data to HPC environments (DeiC WAYF access)

    • DeiC FileSender: Cloud based secured file transfer service (DeiC WAYF access)

  • We rely on a broad range of software solutions and image analysis techniques to find the best fit for your project. We favor open source solutions when available to improve accessibility and reproducibility, but we also consider commercial applications if they bring the most optimal solution for a specific problem.

    Open source bioimage analyis software: ImageJ, QuPath, CellProfiler, ilastik, Python

    Commercial bioimage analysis software: Imaris, Amira, Matlab

  • IACF will seek to share the image analysis workflows and software tools developed (GitHub Repository). Follow the guidelines of the licenses of these projects and don’t forget to cite us and share your feedback as a GitHub Issue or in the relevant section of IACF Forum.

Infrastructure

Register to our Facility and access our Infrastructure

Ask questions of general interest related to our tools

Browse our software tools repository

Training & Events

Past Events

Featured
Call4Help

Call4Help is a bi-monthly public consultation session organized by the DBI-INFRA Image Analysis Core Facility. You can attend these sessions to obtain quick guidance for your bioimage analysis problems and learn from the questions of other peers.

Aarhus University Campus
QuPath workshop
Aarhus University Campus

Are you interested in QuPath for digital pathology?

If so, join us at the University of Aarhus for this free one day workshop (limited seats available)! 

During this hands-on workshop organised on wednesday 17 April 2024, participants will be introduced to QuPath, a powerful user-friendly bioimage analysis software designed to extract quantitative information from microscopy images. QuPath is optimised to process whole slide images from digital pathology, but it can also handle 2D images acquired by most fluorescence microscopes. Common uses include the identification, measurement and classification of nuclei, cells and regions of interest in the images.

Aarhus University Campus
University of Copenhagen
Python4BIA Workshop (2nd edition)
University of Copenhagen

Python quickly became the lingua franca for scientific computing and the recent development of deep learning algorithms. During this 2 day workshop (which does not assume any prior programming knowledge), we will cover Python language essentials and quickly ramp up to bioimage analysis techniques in a hands on fashion. The next segment of the course covers the use and programmatic access to Napari, a powerful nD viewer, and the deployment and training of foundation bioimage analysis deep learning networks such as U-NET and Stardist.

University of Copenhagen

Meet the Team

  • Sébastien Tosi

    BIOIMAGE ANALYST / ELETRICAL ENGINEER (HEAD)

  • Tricia Loo

    BIOIMAGE ANALYST / BIOLOGIST

  • Julia Mertesdorf

    BIOIMAGE ANALYST / COMPUTER SCIENTIST

Contact Us

  • We will be happy to answer any question regarding our service and will try to answer in the shortest possible time!

    iacf [at] dbi-infra.eu

  • DBI-INFRA Hub

    Panum Building, Room 21.1.23

    Blegdamsvej 3B
    Faculty of Health and Medical Sciences
    University of Copenhagen
    DK-2200 Copenhagen N