Advanced Microscopy
Advanced microscopy techniques use laser light, sensitive detection and advanced image processing to obtain high resolution images. Super resolution microscopy methods will generally require more time to obtain the data, because all super resolution methods will require multiple images to be captured and processed. The advantage is that resolution can be 2x -10x more compared to confocal microscopy.
It is advised that the sample preparation is discussed in advance with SLIM staff.
Example Applications & Sample Types
- Bacteria and Biofilms
- Eukaryotic cells
- Subcellular localisation studies
- Extracellular vesicles (EVs)
- Nanoparticles
- Tubulin and cytoskeletal structures
- Actin, mitotic spindle and spindle poles
- RNA in situ FISH
- DNA modifications
- Stem cells and receptors
- Hydrogels and emulsions
- Tissue scaffolds and engineered tissues
- Membrane-labelled cells and bacteria
- Live-cell imaging applications
Advanced Systems
Zeiss Elyra Super-Resolution Microscope
The Zeiss Elyra supports a range of super-resolution and advanced fluorescence imaging techniques for fixed and live-cell applications.
- Structured Illumination Microscopy (SIM) (Elyra 7 SIM2 (NEW))
- STORM 2D & 3D single molecule localisation microscopy
- PALM 2D & 3D imaging
- High-resolution confocal imaging (Elyra PS1)
- Deep tissue and scaffold imaging (Elyra 7 – Apotome (NEW))
- TIRF microscopy for membrane and single molecule imaging
- Temperature control (26–40°C)
- CO₂ compatibility for live-cell imaging
Zeiss LSM 980 & Airyscan2
The Zeiss LSM 980 with Airyscan2 provides advanced confocal and super-resolution imaging with high sensitivity, spectral imaging, and fast acquisition capabilities.
- Point, array and slit scanning confocal imaging
- Widefield imaging capability
- 32-channel Quasar detector for spectral unmixing and capable of online fingerprinting
- Airyscan2 GaAsP detector for super-resolution imaging (~140 nm)
- 4x faster slit scanning confocal imaging (4Y)
- Colibri7 LED light source
- Axiocam 705 mono camera
- Detection range: 405–750 nm
- Temperature incubator (26-40°C)
- Long-term live-cell imaging (e.g. drosophila, biofilm, aerobic conditions).
- Optical z-sectioning of living and fixed samples
- FRET and FRAP experiments
- 3D super-resolution imaging with Airyscan
- Fast confocal imaging workflows
- Photoactivation and photoconversion experiments
- Spectral imaging and advanced spectral unmixing
Nikon NSPARC / TIRF
NSPARC technology is a Spatial Array Confocal scanning application, allowing high speed scanning with greatly reduced laser irradiation allowing low laser power excitation essential for live-cell imaging resulting in less photobleaching and less phototoxicity. The system also provides higher resolution image than conventional point scanning confocal microscopy. The system also incorporates epifluorescece and TIRF microscopy with high sensitivity cameras.
- TIRF imaging for membrane-associated events
- High-sensitivity fluorescence detection
- Live-cell imaging applications with CO2 and temperature control
- Single molecule imaging workflows at low laser power (TIRF)
- Suitable for dynamic cellular processes
- Optical sectioning (3D) and super resolution with NSPARC mode
- Spectral separation is limited since the emission is collected with limited number of band pass filters
SLIM Data Storage & Data Management Guidelines
Guidance for the secure storage, transfer, and management of imaging data generated within the SLIM facility.
SLIM provides temporary data storage to support imaging workflows and data transfer following image acquisition. Users are responsible for ensuring their data is securely backed up and transferred to long-term storage solutions provided by their research group or the 糖心原创.
Data Storage Workflow
1. Initial Data Storage
All imaging data is initially saved locally on the microscope acquisition computer.
2. Data Transfer
At the end of each imaging session, users should promptly transfer their files from the microscope computer to the SLIM Network Attached Storage (NAS).
3. Temporary Storage
The SLIM NAS is provided as a temporary storage solution to facilitate data transfer and short-term access. It is not intended for permanent data archiving.
4. User Responsibilities
Users are responsible for backing up and securely storing their imaging data as soon as possible after acquisition. Users will need to map the SLIM NAS drive folder from their own Desktop PC or laptop to download their files (SOP provided).
5. Data Retention & Deletion
Data stored on the SLIM NAS will be automatically deleted 6 months after upload. Users will receive notification approximately 1 week before scheduled deletion.
6. Microscope Computer Maintenance
Microscope computer hard drives are routinely cleared to maintain optimal instrument and software performance. Any remaining data on the drives will be deleted without prior notice.
Best Practice Recommendations
- Maintain multiple copies of important image datasets.
- Retain the original file type to keep the metadata available (.czi, .nd2 etc)
- Avoid lossy compression (.jpeg etc)
- Transfer data from microscope computers immediately after acquisition.
- Use University-approved long-term storage solutions where possible.
- Regularly verify backup integrity and file accessibility.
- Contact SLIM staff for guidance on data storage and transfer workflows.
Support & Advice
Although users are responsible for managing and storing their imaging data, SLIM staff are available to advise on best practices for data management and available University storage solutions.
Contact
For advice regarding data storage, transfer, imaging data management, data storage plans for grant submissions or data submission along manuscript submissions (data steward advice) please contact:
Robert Markus – Co-Director & Advanced Technical Specialist
Seema Bagia – Co-Director & Advanced Technical Specialist