Klinik für Innere Medizin IHämatologie, Onkologie und Stammzelltransplantation

Lighthouse would like to invite you to the upcoming Technical Workflow Seminar, which will be given by the experts from Thermo Fisher.

Seminar Topics:
• miRNA analysis with advanced TaqMan technologies
• Improved Sanger sequencing workflows with BigDye Terminator Plus
• Olink™ proteomics - up to 5,400 biomarkers from just 1-4 µL sample volume
• Practical tips and application insights from Thermo Fisher Scientific specialists

Date:    June 16, 2026
Time:   10:00 – 12:00
Location: ZTZ, Seminarraum EG, Links

To register for the seminar or for further information, please contact:

Oscar Wiehnholt

oscar.wienholt@thermofisher.com

Tel. 0174 309 1275

Content of the Basic Fortessa Introduction Course

• Principle & construction of a flow cytometer
• Startup operations, operation and shutdown procedures
• Replacement of sheath and waste canisters
• Sample preparation
• Sample measurement
• Sample handling and disposal of GMOs according to the “Gentechnikgesetz (GenTG)”
• Spectral overlap compensation
• Operating FACSDiva software
• Troubleshooting
• Operating booking system and input screen (for billing)
• Optional: More detailed information about FACSDiva & flow cytometry

Since June 2020 we offer the newly designed training courses for the FACS Fortessas and the flow cytometry basics.. 
The regulations for keeping the minimum distance make it impossible to keep the previous training form. Therefore, we were switching to largely contact-free online training. 
If you would like to use our Fortessa flow cytometers and have not yet received instruction on these instruments from us, The events are limited to a max. no. of 2 participants at a time. The introductions can be in German or English. If you require training on this device, please check whether you meet the requirements (registration with the PPMS booking system). Select a suitable date here and apply for training in PPMS via “Request”/“Training Request” and the “Flow Cytometry (FACS) Training Request” form for a binding reservation.

Among them are: 

• several links to instructional videos (total running time about 3hrs)
• an on-site appointment for questions and the short written test

You will then have about 1 week time to watch the videos and fill out forms if necessary.

At an individual on-site appointment for a maximum of 2 persons each (duration in total maximum 90 min.), the formalities are then completed (including a 10-minute written test) and, if possible, permission to use the equipment is granted.

The next dates for the on-site appointments and final exams are planned for:

• 18.06.2026
• 01.07.2026
• 21.07.2026
• 06.08.2026
• 26.08.2026
• 07.09.2026
• 23.09.2026
• 05.10.2026
• 21.10.2026
• 18.11.2026
• 30.11.2026
• 15.12.2026
• to be continued

Content of the CytoFLEX LX Introduction Course

Please note: Successfully participation on our “FACS-Fortessa-Basics-Course” beforehand is mandatory.

You will learn:

• Startup operations, operation and shutdown procedures
• Replacement of sheath and waste canisters
• Sample preparation
• Sample measurement
• Sample handling and disposal of GMOs according to the “Gentechnikgesetz (GenTG)”
• Spectral overlap compensation
• Operating CytExpert software
• Troubleshooting

Since February 2025 we offer the on-site training courses for this flow cytometer.
If you would like to use our CytoFLEX LX flow cytometers and have not yet received instruction on this instruments from us, please send us an email to facslab(ät)uniklinik-freiburg.de with your preferred date for the instruction. You will then receive an email from us with all details and information.

At an individual on-site appointment for a maximum of 2 people each (duration in total maximum 90 min.), the formalities are then completed and, if possible, permission to use the equipment is granted.

The next dates for the on-site appointments are planned for starting at 9:00 AM on:

• 19.06.2026 (auf Deutsch / in German)
• 26.06.2026 (in English)
• 10.07.2026 (in English)
• 17.07.2026 (auf Deutsch / in German)
• 07.08.2026 (auf Deutsch / in German)
• 28.08.2026 (in English)
• 11.09.2026 (auf Deutsch / in German)
• 18.09.2026 (in English)
• 09.10.2026 (auf Deutsch / in German)
• 23.10.2026 (in English)
• 13.11.2026 (auf Deutsch / in German)
• 20.11.2026 (in English)
• 04.12.2026 (in English)
• 18.12.2026 (auf Deutsch / in German)
• to be continued

Content of the Microscopy Trainings

Please note: There are several different microscopy systems available which need selective introductions before usage.

You will learn:

• Startup operations, operation and shutdown procedures
• Sample preparation
• Sample acquisition
• Sample handling and disposal of GMOs according to the “Gentechnikgesetz (GenTG)”
• Spectral overlap compensation
• Operating corresponding software
• Troubleshooting

If you would like to use our widefield, confocal or high throughput systems and have not yet received instruction on this instruments from us, please request a training by send us an email to facslab(ät)uniklinik-freiburg.de with your preferred date for the instruction. You will then receive an email from us with all details and information.

Confocal microscopy basic course (on LSM710/880):

Confocal Microscopy Induction: Course Syllabus 

Systems: Zeiss LSM Series (710/880/900/980) with Airyscan Technology 

I. Theoretical Foundation: The Confocal Principle 

• Physics of Confocality: Understanding the pinhole, optical sectioning, and the rejection of out-of-focus light.
• The Light Path:
  • Excitation: Laser lines and Acousto-Optical Tunable Filters (AOTF).
  • Emission: Secondary Dichroic Mirrors (SDM) and spectral detection.
• Resolution and Contrast:
  • The relationship between Pinhole size (Airy Units) and Z-section thickness.
  • Nyquist sampling criteria for XY and Z.
• Airyscan Technology: Super-resolution concepts (1.7x improvement) and the 32-channel GaAsP detector array. 

II. Hardware Overview & Start-up Procedures 

• The Axio Imager Stand: Introduction to the motorized widefield components (eyepieces, condenser, and internal light paths).
• Objective Care: Proper use of immersion media (Oil, Water, Glycerol) and the critical "cleaning after use" protocol.
• Safe Start-up Sequence:
  1. Main power/Component switches.
  2. Systems/PC initialization.
  3. Laser activation (warm-up requirements).
• Incubation (if applicable): Setting up the heating and CO₂ modules for live-cell imaging. 

III. Software Operation (ZEISS ZEN Blue/Black) 

• The Workflow Concept: Locate (Widefield) vs. Acquisition (Confocal) modes.
• Image Setup:
  • Configuring Smart Setup vs. Manual configuration.
  • Detectors: Setting Gain (Master), Offset, and Laser Power to minimize phototoxicity and bleaching.
• Advanced Acquisition Modules:
  • Z-Stacks: Defining bounds and optimal step size.
  • Tile Scanning: Stitching and focus surface mapping (Definite Focus).
  • Time Lapse: Managing temporal resolution and focus drift.
• Airyscan Processing: Introduction to the "Airyscan Processing" tab and 2D/3D SR reconstruction. 

IV. Data Management & Best Practices 

• The .CZI Format: Why you should always save in the native Zeiss format to preserve metadata.
• Storage Policy:
  • Local vs. Server storage (D: Drive policy).
  • Automatic deletion/cleanup cycles of the facility.
• Metadata: How to retrieve acquisition settings from existing files for reproducibility. 

V. System Shutdown & Quality Control 

• The "Next User" Rule: Checking the facility calendar before complete shutdown.
• Cool-down Protocol: Proper laser venting and shutdown sequence to protect sensitive electronics.
• Hardware Maintenance:
  • Cleaning objectives with lens tissue and Sparkle/Ethanol.
  • Leave the system on lower magnification objective.
• Reporting: How to log hours and report technical issues or hardware errors. 

At an individual on-site appointment for a maximum of 2 people each (duration in total maximum 180 min.), the formalities are then completed and, if possible, permission to use the equipment is granted.

Always watch all videos on this list to be prepared for the course!

The next dates for the on-site appointments are planned from 9:00 -12:00 on:

• (08.06.2026)
• 22.06.2026
• 06.07.2026
• 20.07.2026
• 03.08.2026
• 17.08.2026
• 28.09.2026
• 12.10.2026
• 26.10.2026
• 09.11.2026
• 23.11.2026
• 07.12.2026
• 21.12.2026
• to be continued

Other confocal systems advanced introduction

Zeiss LSM980

Confocal Microscopy Induction: Course Syllabus 

Systems: Zeiss LSM Series (880/900/980) with Airyscan Technology 

I. Theoretical Foundation: The Confocal Principle 

• Physics of Confocality: Understanding the pinhole, optical sectioning, and the rejection of out-of-focus light.
• The Light Path:
  • Excitation: Laser lines and Acousto-Optical Tunable Filters (AOTF).
  • Emission: Secondary Dichroic Mirrors (SDM) and spectral detection.
• Resolution and Contrast:
  • The relationship between Pinhole size (Airy Units) and Z-section thickness.
  • Nyquist sampling criteria for XY and Z.
• Airyscan Technology: Super-resolution concepts (1.7x improvement) and the 32-channel GaAsP detector array. 

II. Hardware Overview & Start-up Procedures 

• The Axio Imager Stand: Introduction to the motorized widefield components (eyepieces, condenser, and internal light paths).
• Objective Care: Proper use of immersion media (Oil, Water, Glycerol) and the critical "cleaning after use" protocol.
• Safe Start-up Sequence:
  1. Main power/Component switches.
  2. Systems/PC initialization.
  3. Laser activation (warm-up requirements).
• Incubation (if applicable): Setting up the heating and CO₂ modules for live-cell imaging. 

III. Software Operation (ZEISS ZEN Blue/Black) 

• The Workflow Concept: Locate (Widefield) vs. Acquisition (Confocal) modes.
• Image Setup:
  • Configuring Smart Setup vs. Manual configuration.
  • Detectors: Setting Gain (Master), Offset, and Laser Power to minimize phototoxicity and bleaching.
• Advanced Acquisition Modules:
  • Z-Stacks: Defining bounds and optimal step size.
  • Tile Scanning: Stitching and focus surface mapping (Definite Focus).
  • Time Lapse: Managing temporal resolution and focus drift.
• Airyscan Processing: Introduction to the "Airyscan Processing" tab and 2D/3D SR reconstruction. 

IV. Data Management & Best Practices 

• The .CZI Format: Why you should always save in the native Zeiss format to preserve metadata.
• Storage Policy:
  • Local vs. Server storage (D: Drive policy).
  • Automatic deletion/cleanup cycles of the facility.
• Metadata: How to retrieve acquisition settings from existing files for reproducibility. 

V. System Shutdown & Quality Control 

• The "Next User" Rule: Checking the facility calendar before complete shutdown.
• Cool-down Protocol: Proper laser venting and shutdown sequence to protect sensitive electronics.
• Hardware Maintenance:
  • Cleaning objectives with lens tissue and Sparkle/Ethanol.
  • Leave the system on lower magnification objective.
• Reporting: How to log hours and report technical issues or hardware errors. 

At an individual on-site appointment for a maximum of 2 people each (duration in total maximum 180 min.), the formalities are then completed and, if possible, permission to use the equipment is granted.

The next dates for the on-site appointments are planned from 9:00 -12:00 on:

• 15.06.2026
• 29.06.2026
• 13.07.2026
• 27.07.2026
• 10.08.2026
• 21.09.2026
• 28.09.2026
• 05.10.2026
• 19.10.2026
• 02.11.2026
• 16.11.2026
• 30.11.2026
• 14.12.2026
• to be continued

Zeiss CD7/LSM900

Confocal Microscopy Induction: Course Syllabus 

Systems: Zeiss LSM Series (880/900/980) with Airyscan Technology 

I. Theoretical Foundation: The Confocal Principle 

• Physics of Confocality: Understanding the pinhole, optical sectioning, and the rejection of out-of-focus light.
• The Light Path:
  • Excitation: Laser lines and Acousto-Optical Tunable Filters (AOTF).
  • Emission: Secondary Dichroic Mirrors (SDM) and spectral detection.
• Resolution and Contrast:
  • The relationship between Pinhole size (Airy Units) and Z-section thickness.
  • Nyquist sampling criteria for XY and Z.
• Airyscan Technology: Super-resolution concepts (1.7x improvement) and the 32-channel GaAsP detector array. 

II. Hardware Overview & Start-up Procedures 

• The Axio Imager Stand: Introduction to the motorized widefield components (eyepieces, condenser, and internal light paths).
• Objective Care: Proper use of immersion media (Oil, Water, Glycerol) and the critical "cleaning after use" protocol.
• Safe Start-up Sequence:
  1. Main power/Component switches.
  2. Systems/PC initialization.
  3. Laser activation (warm-up requirements).
• Incubation (if applicable): Setting up the heating and CO₂ modules for live-cell imaging. 

III. Software Operation (ZEISS ZEN Blue/Black) 

• The Workflow Concept: Locate (Widefield) vs. Acquisition (Confocal) modes.
• Image Setup:
  • Configuring Smart Setup vs. Manual configuration.
  • Detectors: Setting Gain (Master), Offset, and Laser Power to minimize phototoxicity and bleaching.
• Advanced Acquisition Modules:
  • Z-Stacks: Defining bounds and optimal step size.
  • Tile Scanning: Stitching and focus surface mapping (Definite Focus).
  • Time Lapse: Managing temporal resolution and focus drift.
• Airyscan Processing: Introduction to the "Airyscan Processing" tab and 2D/3D SR reconstruction. 

IV. Data Management & Best Practices 

• The .CZI Format: Why you should always save in the native Zeiss format to preserve metadata.
• Storage Policy:
  • Local vs. Server storage (D: Drive policy).
  • Automatic deletion/cleanup cycles of the facility.
• Metadata: How to retrieve acquisition settings from existing files for reproducibility. 

V. System Shutdown & Quality Control 

• The "Next User" Rule: Checking the facility calendar before complete shutdown.
• Cool-down Protocol: Proper laser venting and shutdown sequence to protect sensitive electronics.
• Hardware Maintenance:
  • Cleaning objectives with lens tissue and Sparkle/Ethanol.
  • Leave the system on lower magnification objective.
• Reporting: How to log hours and report technical issues or hardware errors. 

At an individual on-site appointment for a maximum of 2 people each (duration in total maximum 180 min.), the formalities are then completed and, if possible, permission to use the equipment is granted.

The next dates for the on-site appointments are planned from 9:00 -12:00 on:

• 03.06.2026
• 17.06.2026
• 01.07.2026
• 15.07.2026
• 29.07.2026
• 12.08.2026
• 26.08.2026
• 09.09.2026
• 23.09.2026
• 07.10.2026
• 21.10.2026
• 04.11.2026
• 18.11.2026
• 02.12.2026
• 16.12.2026
• 30.12.2026
• 13.01.2027
• 27.01.2027
• 10.02.2027
• 24.02.2027
• 10.03.2027
• To be continued
   

Axio Scan 7

Whole Slide Imaging Induction: Course Syllabus

System: ZEISS Axioscan 7 High-Performance Slide Scanner

I. Introduction to Automated Slide Scanning

• The Axioscan Concept: Moving from manual microscopy to "Digitize & Analyze" workflows.
• Imaging Modalities:
  • Brightfield: For H&E and IHC-stained histology.
  • Fluorescence: High-speed multiplexing (up to 9 channels) using Colibri 7 LED sources.
  • Polarization: Quantitative petrography for geological thin sections or specialized clinical applications.
• Hardware Capabilities:
  • Capacity: Loading up to 100 slides (standard 26 x 76 mm) for 24/7 autonomous operation.
  • Cameras: Axiocam 705 (color) for brightfield and Axiocam 712 (mono) for high-sensitivity fluorescence.

II. Sample Preparation: The Golden Rules

• Slide Integrity: Slides must be clean, free of excess mounting medium, and have no overhanging coverslips.
• Labeling: Best practices for barcodes/QR codes to enable LIMS integration and automated metadata population.
• Tray Loading: Correct orientation of slides in the magazine (up to 25 trays of 4 slides) and ensuring trays are securely seated.

III. System Startup & Software Setup

• Hardware Initialization:
  1. Main Power Supply.
  2. Workstation Boot-up.
  3. Light Sources (Colibri 7 / X-Cite).
• ZEN Slidescan Interface:
  1. Navigating the Magazine View for an overview of all loaded slides.
  2. Scan Profiles: Using "Master" profiles vs. creating custom templates for different tissue types.
  3. Storage Location: Strict policy of saving to the local D: Drive first to prevent network bottlenecks during high-speed acquisition.

IV. The Automated Workflow (Step-by-Step)

• Step 1: The Preview (Pre-scan): Rapid low-magnification overview to locate tissues.
• Step 2: Tissue Detection: Utilizing the Tissue Detection Wizard (or AI-based detection) to automatically define Regions of Interest (ROIs).
• Step 3: Focus Strategy:
  • Setting up focus maps (global vs. local focus points).
  • Autofocus optimization for varied tissue thicknesses.
• Step 4: Acquisition Settings:
  • Brightfield: White balance and shading correction (flat-fielding).
  • Fluorescence: Setting exposure times and "Fast Switching" filter wheel configurations.
  • Z-Stacks/EDF: Extended Depth of Field for thick samples.

V. Post-Processing & Data Management

• The .CZI Ecosystem: Navigating large multi-gigabyte files in ZEN Lite or specialized viewers (e.g., QuPath).
• Stitching & Calibration: Automatic alignment of tiles and system self-calibration for reproducible image quality.
• Data Export: Moving data from local scratch disks to facility servers or cloud storage platforms.

VI. Shutdown & Facility Etiquette

• Safe Unloading: Using the "Unload" command before opening the magazine door to prevent mechanical jams.
• Cleanup: Checking trays for broken glass or leaking oil/medium.
• Shutdown Sequence: Cooling down LED sources and following the designated "Last User" shutdown procedure.
• Error Reporting: How to log issues in the facility management software.

At an individual on-site appointment for a maximum of 2 people each (duration in total maximum 180 min.), the formalities are then completed and, if possible, permission to use the equipment is granted.

The next dates for the on-site appointments are planned from 9:00 -12:00 on:

• 10.06.2026
• 24.06.2026
• 08.07.2026
• 22.07.2026
• 05.08.2026
• 19.08.2026
• 02.09.2026
• 16.09.2026
• 30.09.2026
• 14.10.2026
• 28.10.2026
• 11.11.2026
• 25.11.2026
• 09.12.2026
• 23.12.2026
• 06.01.2027
• 20.01.2027
• 03.02.2027
• 17.02.2027
• 03.03.2027
• To be continued

Lightsheet 7

Light Sheet Fluorescence Microscopy (LSFM) Induction: Course Syllabus

System: ZEISS Lightsheet 7 (Latest 2026 Configuration)

When imaging with the Lightsheet 7, 50% of your success depends on sample mounting. If the sample moves or the Refractive Index is mismatched, the data will be unusable regardless of the software settings."

I. Foundations of Light Sheet Microscopy

• The LSFM Principle: Decoupling the illumination and detection axes to achieve 90° orthogonal imaging.
• Advantages of Light Sheet:
  • Minimal Phototoxicity: Low light dose for long-term live-cell imaging (embryogenesis, organoids).
  • High Speed: Megapixel-per-second acquisition using sCMOS cameras.
• Dual-Sided Illumination: Understanding how the system uses two light sheets to compensate for absorption and scattering in large samples.
• Pivot Scanning: Using the laser "pivot" to eliminate shadows/stripes caused by dense structures in the sample.

II. Sample Mounting & Optics (The Most Critical Step)

• The Sample Chamber: Proper cleaning and assembly of the imaging chamber (trans-illumination vs. fluorescence).
• Refractive Index (RI) Matching:
  • Choosing the correct objective for the medium (Water, Clearing agents like Scale, BABB, or SeeDB).
  • Adjusting the Correction Collar for specific RIs (ranging from 1.33 to 1.58).
• Mounting Techniques:
  • FEP Tubing: For live embryos or organoids.
  • Agarose Embedding: Suspending samples in glass capillaries.
  • Glue/Hooks: For large, cleared whole organs (e.g., mouse brain/kidney).

III. System Start-up & Hardware Configuration

• Power-up Sequence: Components, PC, and Laser modules.
• Objective Installation: Careful handling of the specialized LSFM detection and illumination optics.
• Alignment (Adjust Tool):
  • Calibrating the overlap of the two light sheets.
  • Centering the light sheet in the focal plane of the detection objective.

IV. ZEN Software: Multi-View Acquisition

• The Workflow: "Locate" for sample positioning and "Acquisition" for experiment setup.
• Multi-View Setup:
  • Rotating the sample (360°) to find the best imaging angle.
  • Defining multiple views for later 3D reconstruction/fusion.
• Advanced Modules:
  • Multiside Imaging: Balancing the left and right illumination intensity.
  • Z-Stacks: Setting the start/stop and "Optimal" step size for LSFM.
  • Time Lapse: Managing focus drift and environmental controls (heating/CO₂).

V. Data Management (The "Big Data" Challenge)

• File Sizes: A single experiment can easily exceed 500GB; discussion of the .CZI and BigDataViewer formats.
• Data Streaming: Best practices for writing directly to high-speed SSD arrays (D: Drive) to avoid frame drops.
• Offline Processing: Introduction to Multiview Reconstruction, Deconvolution, and Image Stitching requirements.

VI. System Maintenance & Safety

• Chamber Decontamination: Strict protocols for cleaning after using toxic clearing agents or live biological samples.
• Objective Care: Cleaning the specialized dipping lenses to prevent RI-matching fluid residue buildup.
• Laser Safety: Procedures for a system with an open sample chamber.
• Reporting: Logging usage hours and reporting any leaks or mechanical irregularities in the capillary drive.

Please contact us: Advanced training for Lightsheet 7

We will get in touch with you for a training appointment.

Widefield systems basic introduction (on Axio Imager or Axio Observer or SteREO)

Please contact us: Training for widefield

We will get in touch with you for a training appointment.

High throughput systems introduction (on ScanR, Akoya Phenocycler or IncuCyte)

Please contact us: Training for high troughput

We will get in touch with you for a training appointment.

Online Booking System

Our booking system for our equipment has changeg: All booking calendars are accessible via the internet from outside the Uniklinik intranet. 

Since 1st of February 2026 please use “PPMS” at https://ppms.eu/uni-freiburg-med/login/

Sorter Booking Online

For the cell sorters, you can use the new calendar to look online at current bookings to find an available sorting slot, and you can even request a specific sort time by provisionally reserving a sort appointment in advance. If the requested appointment is accepted, you will receive a written confirmation of the desired appointment. Only then is your sort appointment considered "officially" to be scheduled.

Our new calendar system can be easily accessed, even from outside the Uniklinik network via the Internet. However, to access the system you first have to register as a user in it. For users with an Uniklinik LDAP login the registration process is very straightforward. Using your LDAP login and the corresponding password you can log in. This will automatically send us a request to activate your account. Once your user account has been activated, you might receive a one-time confirmation email from us. After that, you can then use the system.

External users (Vorklinik, University) can also access the system. To do so, please visit https://ppms.eu/uni-freiburg-med/login/?pf=2 and click "user account creation request".

The address of the new Lighthouse booking system can be found at the following link: https://ppms.eu/uni-freiburg-med/