Super-resolution · Zeiss
Our flagship super-resolution platform. Combines Lattice SIM², single-molecule localization microscopy (SMLM/STORM/PALM), and TIRF in one system — with full live cell environmental support for dynamic super-resolution imaging.
Instrument Features
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Lattice SIM²
Second-generation Lattice SIM provides ~120 nm lateral resolution with significantly improved reconstruction robustness over conventional SIM. 5-phase, 5-rotation acquisition with AI-assisted reconstruction reduces artifacts even in challenging samples.
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SMLM — Single Molecule Localization
Supports dSTORM, PALM, and PAINT modalities for nanoscale imaging down to ~20 nm resolution. Thousands of single molecule events are localized and reconstructed into a super-resolution image. Ideal for precise structural analysis of protein assemblies.
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TIRF — Total Internal Reflection
Variable angle TIRF limits excitation to a ~100–200 nm evanescent field above the coverslip. Dramatically improves signal-to-background for membrane-proximal structures, receptor dynamics, vesicle fusion, and cytoskeletal events at the cell surface.
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Live Cell Incubation
Full environmental control (37°C, 5% CO₂, humidity) enables live super-resolution imaging. Lattice SIM² is gentle enough for time-lapse live cell super-res — far less phototoxic than STED or SMLM for extended acquisitions.
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High-Speed sCMOS Camera
Back-illuminated sCMOS camera provides high sensitivity, large field of view, and fast frame rates essential for live Lattice SIM acquisition and SMLM blinking event capture.
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Multimode Flexibility
Switch seamlessly between Lattice SIM², TIRF, and SMLM modes within a single session. Combine widefield, TIRF, and super-resolution channels on the same sample for correlative experiments.
Startup Guide
Power On in the Correct Order
Turn on the laser launch box first, then the electronics box, then the PC. Order matters — follow the posted startup sequence on the instrument. Allow 20–30 min warm-up for laser and camera stabilization.
Launch ZEN Black (Elyra)
Open ZEN Black with the Elyra configuration. Select your imaging mode: Lattice SIM², SMLM, or TIRF. Wait for full hardware initialization.
Activate Lasers
Enable required laser lines. For SIM, laser stability is critical — allow full warm-up before starting calibration or acquisition. For SMLM (dSTORM), activate both the imaging laser (e.g., 647 nm) and activation laser (405 nm).
Select Objective
Use the 63×/1.4 Oil Plan-Apochromat for standard Lattice SIM. Use the 100×/1.46 Oil for TIRF and SMLM experiments requiring maximum evanescent field control. Apply high-refractive-index immersion oil.
Load Sample
Mount your #1.5H coverslip preparation on the stage. For live imaging, allow incubation chamber to reach 37°C / 5% CO₂ before loading. Ensure no air bubbles between coverslip and objective.
Navigate & Focus
Use widefield or TIRF live view to find your cells. For SIM, find a cell near the coverslip surface (within 10–15 µm for best results). Use the definite focus system to lock Z-position for live experiments.
Configure Lattice SIM²
Select Lattice SIM² acquisition. Set 5 phases × 5 rotations. Adjust laser power (keep as low as possible for live cells). Set Z-stack interval using the Nyquist calculator. Run a test acquisition and check SIM quality using the SIM check tool before full acquisition.
Configure TIRF Angle
Adjust the TIRF angle slider until you reach the critical angle — you will see a dramatic increase in signal-to-background as surface-proximal fluorophores light up and cytoplasmic background disappears. Fine-tune for maximum contrast.
Configure SMLM Acquisition
For dSTORM: use high laser power (>1 kW/cm²) to drive fluorophores into dark state. Set 405 nm activation laser to low power (~0.1%). Acquire 10,000–50,000 frames. Use ZEN’s ThunderSTORM or built-in SMLM analysis for reconstruction.
Acquire & Process
Run full acquisition. For SIM data, apply SIM processing in ZEN (Processing tab). For SMLM, run localization analysis. Save all raw and processed data before logging off.
Shut Down
Turn off lasers first, then electronics box, then PC. Remove sample, clean objective with lens paper. Do not leave high-power lasers running unattended.
⚠️ Refer to the Elyra 7 Sample Preparation Guidelines (main page) before your session. EM-grade fixation, pre-mount DAPI staining, #1.5H coverslips, and Prolong Diamond/Glass or Abberior Mount Solid are required for optimal SIM quality.