Zeiss Elyra 7 – Lattice SIM

Location: I24.U1.031 (Moonstone)

Zeiss Elyra 7 Lattice SIM (Structured Illumination Microscope) is a multi-modal Super Resolution microscope with a climatized chamber, humidity – CO2 and O2 control. The different modalities (Lattice SIM, SIM2, SMLM, TIRF, Apotome) allow imaging across scales from down to 60 nm. The adaptive optics allow to adjust to the different refractive indices (RI).

Imaging modes:

  • Lattice SIM: 3D Super-resolution Live Cell Imaging using Structured illumination + image reconstruction
  • Lattice SIM²: SIM² is an image reconstruction algorithm that increases the resolution and sectioning quality of structured illumination microscopy data. SIM² is compatible with all SIM imaging modes of your Elyra 7 and fully integrated in the ZEN software.
  • SIM² Apotome and Leap Mode: Iaging modes for  improved lateral and axial resolution as well as volume acquisition speed while being very gentle to the sample. Leap mode accelerates the volume imaging speed three times and at the same time decreases the light dosage on the sample for both Lattice SIM² and SIM² Apotome modes.
  • SMLM: Single molecule localization microscopy including drift correction and localization algorithms
  • TIRF: total internal reflection microscopy 

System Manual including SIM and Batch processing


  • Climatized chamber, humidity – CO2 and O2 control.
  • 4 laser lines (405, 488, 561, 642nm)
  • dual-link camera (PCO edge sCMOS), up to 255 fps( burst / leap mode)
  • Automated axis XYZ+ rotation
  • Multi-position & tiling
  • Additional piezo driven z-axis for fast imaging


  1. EC Plan-Neofluar 10x / NA 0.3 M27 WD 5.2 mm (420340-9901-000)
  2. Plan-Apo 20x / NA 0.8 WD 0.55 mm (440640-9903-000)
  3. EC Plan-Neofluar 40x / NA 0.75 WD 0.71 mm (440350-9903-000)
  4. Plan-Apo 63x /NA 1.4 Oil DIC M27 WD 0.19 mm (420782-9900-000) for Lattice SIM imaging
  5. alpha Plan-Apochromat 63x/1,46 Oil Korr M27 WD 0.1 mm (420780-9971-000) for TIRF imaging
  6. C-Apochromat 63x / NA 1.2 W korr UV-VIS-IR WD 0.28 mm (421787-9970-799)

Light sources

  • X-cite Xylis XT720L for epi-fluorescence imaging: FSet77 HE fluorescence filter for all colors
  • Elyra Laser Module: laser lines:405nm, 488nm, 561nm, 640nm

Filters / Beamsplitters

Filter cubes for epif-luorescence: FSet77 HE fluorescence filter for all colors

  • LBF 405/488/561/642
  • BP 420-480 + BP 495-525 + LP 655
  • BP 495-550 +BP 570-620
  • BP 420-480 + LP 655

Dichroic Mirrors to split between the two cameras

  • SBS LP 560
  • SBS BP 490-560 + LP 640


Zeiss ZEN black SR

  • Tiles & Positions
  • ZEN Toolkit Smart Acquisition
  • ZEN Toolkit 2D
  • ZEN Toolkit 3D
  • ZEN Toolkit Connect
  • ZEN Module Lattice SIM / SIM²
  • ZEN Module Super-resolution Localization Microscopy
  • ZEN Module 3D-PALM
  • ZEN Module sequential Dual-Color PALM

Computers Workstations

Microscopy Workstation Premium hp Z6 G4

  • Graphics Card NVIDIA RTX A5000
  • Hard Drive Extension 12TB RAID10
  • HP Z6 G4 Rev. 2 Workstation

Storage and Data Analysis PC 81 TB w/

  • Graphics Card NVIDIA RTX A5000