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Center for Integrative Infectious Disease Research (CIID)

We believe we can reveal better medical treatments and develop a comprehensive understanding of physiology of important human pathogens by integrating holistic and reductionist experimental approaches.



Classical biochemical, genetic and genomic approaches have been employed over the years to yield important insights in host-pathogen interactions. Most of these experimental approaches are population-based (“bulk”), end-point analyses where obtained information represents an average across the population and where important parameters can be missed as they become “averaged out” in the bulk measurement. The different states of biological systems, such as for example, the differences between the health and the disease state, are ultimately governed by the individual, stochastic and often rare molecular events. We believe that to truly understand different physiological states, we need to employ a reductionist experimental approach that is able to capture and quantitatively examine these individual molecular events. Such information can than be incorporated into mathematical models together with the observations made using the population-based approaches ultimately leading to a comprehensive understanding of the underlying patho-physiological processes.

Why microscopy?

Due to recent innovations, the only methodology able to capture and quantitatively examine individual molecular events in a complex biological system is microscopy-based imaging. A microscope can sample complex dynamics of a biological system across a wide range of spatiotemporal scales and organizational levels of complexity, and thus is able to provide the most realistic representation of a living system. It is a big technical challenge to observe and quantify these stochastic molecular events. An equally big  challenge is to understand how they give rise to different stereotypical patho-physiological states that we observe in “bulk” measurements. In this respect, microscopy-based analysis yields quantitative information that can be integrated into predictive multiscale mathematical models of infection that will ultimately be used to reconcile the findings obtained by the reductionist approach with the ones that are based on population measurements. 

What is IDIP?

The Infectious Diseases Imaging Platform (IDIP) provides, develops and applies high-end microscopy infrastructure under conditions of enhanced biosafety containment 2 and 3 (BSL-2 and 3) to enable infectious diseases research. IDIP is part of the Center for Integrative Infectious Disease Research (CIID), University Hospital Heidelberg, Germany as well as German Center for Infection Research (Deutsches Zentrum für Infektionsforschung, DZIF)


Over 250m  of the ground (BSL-2) and underground (BSL-3) area of the CIID is dedicated to the IDIP infrastructure. The IDIP infrastructure is organised in 14 interconnected microscopy rooms, tissue culture and sample preparation, image analysis, visitor and office areas. IDIP implements a comprehensive range of bioimaging technologies that allow infectious disease research across vastly different spatiotemporal scales and organizational complexities, going from structural studies on macromolecular scale all the way to whole organ/body imaging in living animals. Click here for more information about IDIP organisation and instrumentation.


Whant to kow more about IDIP?
Check these videos
Short video: Interview with the Head of IDIP
Long video: Interview and IDIP tour

/IDIP usage workflow

This is a workflow of a typical microscopy-based experiment. Potential users can interact with IDIP by seeking consultation, training, infrastructure etc. during some or all stages shown here

IDIP workflow2.jpg

- Consultation on experimental setup

- Choice of instrument

- Support for related grants applications

- Formalities

- Biosafety...

- Instrument training

- Acquisition optimisation (3D, multichannel, temporal and spatial resolution…)

- Automated microscopy…

- Specialized software training

- Type of analysis (object counting, tracking, intensity measurements, colocalization…)

- Analysis automation, macros/plugins development…

- Choice of dyes, fluorescent proteins, markers

- Fixation protocols

- Live cell compatible reagents…

- Data storage

- Deconvolution

- Data processing for visualisation and quantification

- Ethical guidelines

- Image processing software training…

Becoming a user

/becoming a user

Who can become a user?

Internal Users

Primary IDIP users are members of the Center for Integrative Infectious Disease Research (CIID), Center for Infectious Diseases of the University Hospital Heidelberg and other members of Heidelberg University campus that need microscopy infrastructure under enhanced biosafety conditions. Members of organisations which co-finance IDIP infrastructure, such as the Heidelberg University Field of Focus 1 network and the German Center for Infection Research (Deutsches Zentrum für Infektionsforschung, DZIF), are also considered as “internal users”.


External Users

The IDIP infrastructure is also open to “external users”. They include interested investigators from other academic research institutions and collaborators from industrial partners.

How to become a user?

Prerequisits for access to IDIP:

- necessary biosafety training needs to be accomplished (level 2 or 3 depending on the pathogen and experimental setup used)

- Experiments with primary human or animal material that require evaluation by an Ethics committee can only be conducted after a respective Ethics vote has been obtained by the responsible Ethics Committee (in most cases the Ethics Committee of the University Hospital Heidelberg).

- IDIP registration needs to be completed

The registration process

Create personal IDIP account using the following link:

Choose "Account creation request", fill out the form and click "Submit"

Go to your newly created personal IDIP account at and login. Choose "Training request". Fill and submit the form.

Initial discussion and training will be arranged by IDIP staff in collaboration with the user

Training is conducted by IDIP staff

Congratulations! You can now book the required system using your personal IDIP account at

User fees

/User fee system

Different user fees apply for “internal” and “external” users.


The user fees for internal users cover the specific, project-related, instrument operating costs, adaptations, upgrades and replacements, instrument-related consumables as well as project-specific staff costs within the framework of the applicable third-party funding agency guidelines.  This is in accordance with the DFG guidelines for Research Infrastructure for Advanced Light Microscopy which can be found here.


Indirect costs (electricity, cleaning, general room maintenance etc.), VAT, instrument depreciation and costs of IDIP staff connected to routine infrastructure maintenance are not covered by user fees.


The fee for external users includes operating costs, full staff costs, indirect costs (40% overhead) and VAT (19%) in addition.

Mote details about the pricing and user fee system can be found here.

To keep the IDIP infrastructure operational it is necessary to raise necessary funds. This is partly done through user fees and partly through institutional and third party funding. Funds to cover usage fees can be requested as part of grant proposals to the DFG, the BMBF and the European Commission. Guidelines for requesting usage fees have been published by the DFG and can be found here (English) and here (German). 

Rules and regulations

/rules and regulations

General rules

Relevant biosafety, work safety and laser safety instructions must be followed.

Find detailed IDIP usage rules, including microscopy-specific biosafety, laser safety and gas safety instructions here.

Before using any IDIP instruments registration and training must be requested and completed accordingly. Register here.


Booking of the equipment including image processing workstations before usage is obligatory without exception. Even if the equipment is momentarily free it needs to be booked before usage. 

Management of the acquired data is at the sole responsibility of the user. Data are allowed to remain stored on the system’s local hard drive for 2 weeks after which they will be automatically deleted. More details including recommendations on data handling can be found here.

Equipment usage rules

Any equipment as well as microscopy rooms have to be handled with great care. 

Access to a particular instrument within IDIP is restricted to registered and trained users exclusively. Non-registered users can accompany registered users under the registered user's responsibility. Non-registered users are not permitted to work or stay at microscope systems in absence of a registered user.

Before use the instrument needs to be visually inspected. Damage or problems need to be reported to the IDIP staff immediately.

If anything unusual is observed during use (such as strange or loud sounds, alarm, smoke, explosion etc.) the room needs to be vacated immediately and occurrence reported to the IDIP staff.

After usage - objective lenses, stage area and bench area need to be cleaned and all personal items removed. The microscopy infrastructure has to be left after use in the same condition as provided and must be free of any kind of contamination.

After finishing the session, the user needs to check if the system is booked later on the same day and if not the last user needs to switch off the instrument.

The user needs to report any problems or damages occurred during his/hers session by submitting an "incident report" using the online booking system.

Parts or documents belonging to the equipment must not be taken out of the room where the instrument is located.

Booking rules

Booking of the equipment including the image processing workstations before usage is obligatory without exception. Even if the equipment is momentarily free it needs to be booked before usage. 

Booking is performed exclusively via the online IDIP booking system using the personal account.

Equipment cannot be booked more than 2 weeks in advance, not more than 3 times a week and each booking slot must not exceed 4 hours. If longer time slots are required or more long-tern planning of experiments is required, IDIP staff must be contacted.


Long lasting experiments (long time lapses) should be scheduled outside peak usage hours (between 18:00 – 9:00). A deviation from these rules is possible if a particular experimental setup demands it. Any deviation needs to be approved by the IDIP staff.

Booking can be deleted or edited up to 2 days before the booked date without consequence. If the booking is deleted or edited less than 48h before the booked time, user fee charges may still apply (see user fee section for more details).

Any deviation from these rules needs to be approved by IDIP staff.

< 2 weeks
< 3 x week
< 4h per day
Publication and acknowledgment policy

If published results were acquired/analysed using the IDIP infrastructure (e.g. microscopes, workstations, software etc.) and/or IDIP staff consultation services a statement in the form “We would like to acknowledge the microscopy support from the Infectious Diseases Imaging Platform (IDIP) at the Center for Integrative Infectious Disease Research, Heidelberg, Germany” needs to be entered in the acknowledgment section of the publication and a pdf of the published paper needs to be sent to the Head manager of the IDIP for internal quality management and reporting to the granting agency.

If IDIP staff is actively involved in research projects in a collaborative manner beyond providing basic IDIP infrastructure and consultation, respective IDIP members are regarded as co-authors in the respective publication in addition to the acknowledgment statement.

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