Zeiss Elyra PALM/SIMS Superresolution

The Zeiss Elyra PALM/SIM Superresolution Microscope is a dual system built around a Zeiss Axio Observer.Z1 inverted microscope and specially designed for super-resolution microscopy techniques.

The first modality available is Serial Localization Microscopy, better-known by the two main techniques, Photoactivation and Localization Microscopy (PALM) and Stochastic Optical Reconstruction Microscopy (STORM. Data are collected with a high-sensitivity Andor iXon 897 EMCCD cameras for rapid acquisition of images with capabilities to localize molecules in 2D or in 3D using the prism that modulates the PSF (point spread function).

The second modality is Structured Illumination Microscopy (SIM). With this technique, images of twice the resolution of conventional microscopy in all 3 dimensions are possible. This system has a devoted Andor iXon3 885 EMCCD camera for high-sensitivity imaging with a wide field of view in SIM mode. The Elyra system contains illumination gratings for each of the system’s objectives and laser wavelengths, allowing for a wide range of fluorophores and length scales. The microscope stage is enclosed in an environmental control chamber for live-cell imaging. Zeiss’s ZEN software is included on the system for image acquisition as well as on standalone machines for post-processing of superresolution images.

Microscope body:
Motroised Stage:
Temp Control:
Fully enclosed
Zeiss Zen 2012

Common Applications


Stochastic Optical Reconstruction Microscopy is a super-resolution microscopy technique utilising a TIRF architecture to illuminate the first 100-200 nanometers of a sample and image single fluorescent molecules as they are first converted from a dark to active state by an appropriate buffer solution, before bleaching a short time later. At any time only a very small portion of the fluorophores are active and with each dark-active-bleach cycle more and more of the underlying sample is revealed at up to 10x the resolution of conventional techniques.

PALM: Photo-activated localization microscopy is a super-resolution microscopy technique where the principle of detection and analysis is the same as STORM, but in this case it is not anti-body based labelling and does not require special buffers, but rather requires use of photo-activable genetically encoded proteins.

This method involves illuminating a fluorescent sample with an illumination pattern, here a series of light and dark bands. After acquiring a series of images with the illumination pattern in different orientations, spatial information about the sample that normally would be lost, can be yield. It requires at least 3 rotations (optional 5) and 5 phase images for a total of 15 (or 25) images in order to reconstruct one super-resolution image. As such it makes this technique compatible with live cells imaging but for intermediate to slow dynamical processes.


Objective Lenses

10x 0.3 EC Plan-Neuofluar AIR 5.2 mm  
63xx 1.4 Plan-Apochromat OIL 0.19 mm DIC
100x 1.46 alpha Plan-Apochromat OIL 0.11 mm DIC

Light Sources

Source Wavelengths Nominal Power
HR Diode 405 50 mW
HR Diode 488 200mW
HR DPSS 531 200 mW
HR Diode 642


160 mW
TX-Cite Lumen Dynamics 

UVX 375 - 400, BDX 450 - 495, GYX 540 - 600

Transmitted illumination White light  



Filter Wheel 1
      BP 420-480/ LP 750
      BP 495-575/ LP 750
      BP 570-650/ LP 750
      LP 655


Filter Wheel 2
LBF 405/561      
LBF 405/488/642      
LBF -561/642      
LBF -488/561      



Application Model Pixel Format Sensor Type Readout Speeds (MHZ) Description
PALM/STORM Andor iXon 897 512x512 (16 µm pixel size) EMCCD 1, 3, 5 and 10

Sensitivity and speed at 30 fps at full 512x512

SIM Andor iXon3 885 1004x1002 (8 um pixel size) EMCCD 13, 27 and 35 Sensitivity and speed at 31.4 fps at full 1004x1002