IACF Services

Our team of experts is here to discuss your image analysis needs, guide and train you in the most suitable software solutions, or 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.

Image Analysis Workflow Development

  • We offer tailored software and workflow development for bioimage analysis projects of varying scope and complexity and across different image modalities, including microscopy, pre-clinical and clinical data.

    Typical projects include:

    • Automating repetitive image processing tasks with custom scripts or macros

    • Building end-to-end analysis workflows that integrate multiple tools or programming languages

    • Developing machine learning or deep learning–based approaches for complex datasets

    For larger-scale projects or advanced computing needs, we collaborate with Computer Science research groups at KU and DTU and can help connect you with the right partners, if your project exceeds our scope.

    Development begins with a free consultation and is billed at an hourly rate listed under Rates (Academic Users) below. Once your tool or workflow is complete, we provide tailored training - either in-person or remotely - to ensure you can use it effectively.

    For more details on how to apply and get started, please refer to our User Guides under the User Access section in the side menu.

  • Already developed a workflow but want to validate, improve or optimize it? We offer expert support in reviewing and refining your existing scripts, macros, or pipelines. This includes:

    • Debugging and performance optimization

    • Improving code readability and documentation

    • Updating workflows to align with best practices and current tools

    • Scaling up your workflow for batch analysis

  • Over the years, the IACF has collaborated with researchers to develop a wide range of custom workflows and software tools tailored to specific scientific questions. These projects span from simple automation scripts to complex pipelines involving machine learning. You can browse selected projects and tools in our Project gallery, which is regularly updated with new case studies.

Software Tools and Training

  • We offer personalized training in a wide range of bioimage analysis tools to support researchers at all experience levels. Training sessions are tailored to your specific project needs and can be conducted in person or remotely.

    Our training covers:

    • Hands-on guidance with our supported software tools, adapted to your imaging data and research question

    • Techniques for visualizing, publishing, and preserving scientific images to ensure high-quality outputs

    • Access and support on our bookable analysis workstations (in person or remote)

    For more details on how to book a training session and get started, please refer to our User Guides under the User Access section in the side menu.

  • We offer training in a broad range of software solutions and tools 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 software: ImageJ, QuPath, CellProfiler, Ilastik, Python, Cellpose, Napari

    Commercial software: Imaris, Amira (2019), Matlab, Arivis Vision 4D (v. 3.5)

Computational Infrastructure

  • 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 Workstation Specs (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).

  • We provide access to secure, high-performance computing resources through UCloud, a remote platform that allows to run image analysis tools from the browser, without needing to install any software locally on a computer. UCloud can be used either through an intuitive remote desktop interface (Linux), or run large-scale analyses without user interaction via headless batch processing. UCloud environments are private, GDPR-compliant, and tailored to meet the needs of academic research.

    UCloud is ideally suited for long-running, CPU- or GPU-intensive tasks using open-source software — making it the preferred solution for scalable, high-performance analysis workflows.

    • Please note: Access is only available through DeiC WAYF to researchers affiliated to a Danish institution.

    The IACF offers dedicated training and support to help you get started with UCloud, including how to access it, run your analyses, and work efficiently within the platform.

Access IACF Services

Not sure about what you need? Struggling to define your image analysis problem? Just have some quick questions?

Join our free public consultation, happening every alternate Thursday.

Free Consultation

Call for Help

Rates (Academic Users)

Windows Workstations: 150 Kr/h

Personal Training/Support: 500 Kr/h

Software development: 750 Kr/h

    • 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 finetuning (16h Dev. + 2h training): 12.100 Kr

    • Multi-Component IA Workflow Development (40h Dev. + 4h Training): 26.000 Kr

    • According to Danish Competition Law, Commercial Usersare 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)

Terms of Service

    • 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.

    • IACF is the owner of the code/software developed, and will make them publicly available on an IACF-managed code repository within a year of project completion, and in accordance with open science and FAIR data principles. The IACF may agree to coordinate the publication of such code/software with the publication of the generated scientific data

    • 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.

  • 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)

    • 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.