University of Gothenburg
Elyra 7 Lattice SIM
Photo: Rafael Camacho CCI

ELYRA 7 with Lattice SIM and SMLM

The Carl Zeiss ELYRA7 is a state-of-the-art inverted widefield microscope designed for fast (Super-resolution) live-cell imaging via Lattice Structured Illumination Microscopy (SIM) and single-molecule localization microscopy (SMLM).

The Elyra 7 microscope

The ELYRA 7 microscope is a widefield inverted microscope designed for high-speed super-resolution imaging of biological specimens with minimal light exposure. It is equipped with an incubation system (temperature and CO2 control) and a dual camera adapter that houses two sCMOS cameras (PCO edge) for imaging two channels simultaneously.

The ELYRA7 is capable of out-of-focus light suppression and sectioning via the Apotome module and doubling the resolution of conventional widefield via Lattice Structured Illumination Microscopy (SIM). Novel image processing and imaging modalities like Burst and Leap modes can be used for increased speed and efficiency during imaging. Further, the ELYRA7 also allows for Single Molecule Localization Microscopy (SMLM) techniques such as PALM, dSTORM, and PAINT. SMLM is available with high-power lasers across the visible spectrum giving access to a broad range of fluorescent markers.

Elyra 7 micrsocope
Photo: ZEISS
Light pattern example
Photo: Rafael Camacho CCI

Imaging modalities of the ELYRA 7

Imaging with a widefield system suffers from out-of-focus blur or background signal. These effects can decrease contrast and resolution of your images. The SIM Apotome acquisition mode uses structured illumination to give a fast optical sectioning with crisp contrast and high lateral and axial resolution. This is compatible with live cell imaging of large areas at speeds much faster than classical confocal, and contrast well above standard widefield microscopy.

The ELYRA 7 SIM2 Apotome is superior to conventional confocal microscopy in terms of lateral and axial resolution as well as volume acquisition speed while it is also compatible with gently live cell imaging. The Leap mode accelerates the volume imaging speed three times and at the same time decreases the light dosage on your sample.

In Lattice SIM, the sample is illuminated with a lattice spot pattern instead of grid lines as in conventional SIM, leading to an increased imaging speed. In addition, the lattice pattern provides higher contrast, which allows more robust image reconstruction. Due to the Lattice SIM pattern, you need less laser dosage for sample illumination compared with classical SIM. The increased the imaging speed while achieving higher contrast and lower photo dosage, make Lattice SIM compatible with live cell imaging experiments.

SIM² is the novel, image reconstruction algorithm from ZEISS 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.

With 500 mW laser modules, the Elyra 7 is a very flexible laser widefield system that can be used for many applications such as single-particle-tracking and single-molecule-bleaching. The system has the capacity of doing HILO and TIRF illumination, which reduces the illumination volume and removes out of focus light. In these methods, the illumination is limited to a few microns close to the glass surface.

SMLM encompasses techniques such as PALM, dSTORM, and PAINT. With high power lasers across the visible spectrum and dual camera detection, the Elyra 7 allows SMLM with a broad range of dyes, markers and fluorophores.

Photo: Rafael Camacho CCI
Photo: Rafael Camacho CCI
Photo: Rafael Camacho CCI

Elyra 7 system characteristics

Objective lenses

Air objectives (Apotome)

Immersion objectives (SIM, SMLM)

Light sources


  • HR Diode 405 nm 50 mW
  • HR Diode 488 nm 500 mW
  • HR Diode 561 nm 500 mW
  • HR Diode 642 nm 500 mW

Fluorescent Lamp

  • HXP fluorescent lamp

Note: Elyra 7 is capable of TIRF illumination for laser widefield and SMLM


Reflector module:

Filterset 1: Flexible

  • LBF 405/488/561/642 (QUAD)
  • Excitation 405/488/642 Emission BP 420-480 + BP 495-550 + LP 655
  • Excitation 488/561 Emission BP 495-550 + BP 570-620
  • Excitation 405/642 Emission BP 420-480 + LP 655

Filterset 2: Pure

  • LBF 405/488/561/642 (QUAD)
  • Excitation 405 Emission BP 420-480
  • Excitation 488 Emission EF BP 495-590
  • Excitation 561 Emission EF LP 570


  • SR Quad: Position 1 LP 560 | Position 2 BP 490-560 + LP 640
  • SR DUO: Position 1 LP 560 | Position 2 LP 640


Duolink adapter to operate two sCMOS cameras:

  • pco.edge 4.2 CL HS sCMOS camera, 6.5 µm pixel size, peak QE 82%, liquid cooled