/mission
Center for Integrative Infectious Disease Research (CIID)
Our vision
We aim to achieve a comprehensive understanding of host–pathogen interactions and the mechanisms underlying infectious disease through the development and application of advanced imaging approaches. By resolving individual molecular and cellular events in space and time, we seek to quantitatively characterize the processes that determine different physiological and pathophysiological states and to use this knowledge to inform the development of improved therapeutic strategies.
Traditional biochemical, genetic and “omics” approaches have provided fundamental insights into host–pathogen interactions, but many of these methods rely on population-level measurements or endpoint analyses. Such approaches can obscure rare, transient or stochastic events by averaging them across large populations. Yet these individual events can be critical determinants of cellular behaviour and may drive transitions between healthy and diseased states.
We therefore aim to complement population-based approaches with a reductionist strategy at the level of individual molecular and cellular events. By resolving, quantifying and mechanistically characterizing these events in their spatial and temporal context, we can gain a more detailed understanding of complex pathophysiological processes. Integrating these measurements with population-level observations and mathematical modelling will ultimately allow us to build a more comprehensive understanding of host–pathogen interactions and disease mechanisms.
Why microscopy?
Due to recent technological advances, microscopy-based imaging is uniquely capable of capturing and quantitatively examining individual molecular and cellular events within complex biological systems. A microscope is unique in its ability to:
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show us what things look like and where they are — revealing the structure, morphology and spatial organization of living matter, from molecules and organelles to cells, tissues and pathogens;
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tell us how much is where — providing quantitative information on the abundance and distribution of biological components; and
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show us how things change over time — capturing the dynamics of living systems.
Structure, spatial organization and function are intimately connected across all scales of biological organization. The three-dimensional structure of a molecule determines how it interacts with its environment; cellular morphology reflects and enables specialized functions; and the organization of tissues and organs emerges from the functions they perform. By preserving these structural relationships while simultaneously providing quantitative and temporal information, advanced imaging offers a uniquely rich description of biological systems.
A modern microscope is therefore much more than an instrument for taking pictures. It is a robotic system capable of systematically sampling the complex dynamics of biological systems across a wide range of spatial and temporal scales and levels of organization. This makes advanced imaging one of the most powerful approaches for obtaining a realistic representation of biological processes in their native context.
Observing and quantitatively characterizing rare and stochastic molecular and cellular events is a major technical challenge. An equally important challenge is understanding how these individual events collectively give rise to the stereotypical physiological and pathophysiological states observed in population-level measurements. Microscopy provides a bridge between these scales. Imaging-derived measurements can resolve individual molecular and cellular events while retaining their spatial and temporal context, and can be integrated with population-level observations and predictive multiscale mathematical models. Such integration can help connect the behaviour of individual components to the emergent properties of cells, tissues and organisms, providing a framework for reconciling reductionist measurements with the complex phenotypes observed at the population and organismal levels.
What is IDIP?
The Infectious Diseases Imaging Platform (IDIP) develops and applies advanced imaging approaches and high-end microscopy infrastructure under enhanced biosafety conditions (BSL-2 and BSL-3) to enable infectious disease research. IDIP is part of the Center for Integrative Infectious Disease Research (CIID) at University Hospital Heidelberg, Germany, and is integrated into the German Center for Infection Research (Deutsches Zentrum für Infektionsforschung, DZIF).
More than 250 m² of ground-floor (BSL-2) and underground (BSL-3) space within the CIID is dedicated to IDIP. The infrastructure comprises 14 interconnected microscopy rooms, tissue culture and sample preparation facilities, image analysis workstations, as well as visitor and office areas.
IDIP encompasses a comprehensive range of advanced bioimaging technologies, enabling infectious disease research across a broad spectrum of spatial and temporal scales and levels of biological organization — from structural studies at the macromolecular scale to imaging of entire organs and living animals. This breadth allows biological processes to be investigated across scales, using appropriate imaging technologies and experimental models.
Click here for more information about IDIP organisation and instrumentation.
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Whant to kow more about IDIP?
Check these videos
Short video: Interview with the Head of IDIP
Long video: Interview and IDIP tour
Short video: Examples of projects conducted in IDIP
/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
Strategy
Sample
preparation
Data
acquisition
Data
processing
Data
analysis
- 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
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”. A project can be conducted in IDIP if it fulfilles at least ONE of the following criteria:
- the project requires BSL2/BSL3 containment
- the project is in the field of infectious diseases research
- there is no comparable instrumentation in other facilities on the campus
External and Company 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). For internal users the training is done by the respective PI and for the external users by IDIP staff.
- 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: https://ppms.eu/idip-heidelberg/login/?pf=2
Choose "Account creation request", fill out the form and click "Submit"
Go to your newly created personal IDIP account at https://ppms.eu/idip-heidelberg/login/?pf=2 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 https://ppms.eu/idip-heidelberg/login/?pf=2
/User fee system
Different user fees apply for “internal”, “external” and "company" 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, administration, etc.), routine instrument maintenance, instrument depreciation and costs of IDIP staff connected to routine infrastructure maintenance and VAT are not covered by fees for internal users.
The fee for external users includes full operating and staff costs with 19% VAT, while fees for company users include indirect costs (40% overhead) and depreciation costs 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.
/rules and regulations
General rules
Relevant biosafety, work safety and laser safety instructions must be followed.
Find detailed IDIP usage rules 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.
Register
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 17:00 – 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 24h 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.