UltraMicroscope – II La-vision

The UltraMicroscope  II by La-Vison is a commercialized lightsheet microscope, this is a fluorescent microscope designed for large samples that were usually cleared for imaging using one of the various available protocols.
The ultramicroscope is unique in its ability to image samples clarified in a wide range of refractive index media, from water to organic solvents based protocols.


Lightsheet Z1 - Zeiss

The Lightsheet Z1 by Zeiss is a commercialized lightsheet microscope, this is a fluorescent microscope designed for relatively large live samples for long term time laps, in gentle imaging conditions (relative to conventional confocal microscopy).
The unique Lightsheet Z1 design enables to image samples of three dimensional structures without distortion with close to isotropic resolution in all three axes (X,Y,Z).
The 3D characteristics are also highly valuable for imaging of water based cleared samples of organisms or organs.
Z1 LightSheet on Zeiss site


Confocal–MultiPhoton - Leica TCS SP8

The Leica TCS SP8 Confocal – MultiPhoton is a powerful two photon microscope, based on a high end confocal.

The microscope is aimed to work on thick live or fixed samples in 2D, 3D and 4D.
The combination of high power tunable laser with highly sensitive detectors allows deep penetration into thick tissue, and image high resolution fluorescence and Second Harmonic images.
Based on an upright configuration equipped with a Chameleon Vision II - Coherent tunable ultra fast Ti:Sapphire laser 680-1080 nm. 3 internal spectral detectors and 3 NDD detectors.


SmartClear II - Lifecanvas

SmartClear II ( Based on Stochastic Electrotransport method, this technology allows for significant reduction in preparation time (from~2 weeks to ~2 days, depending on tissue type) and better preservation of the tissue.

Alongside, we provide also the relevant buffers: Clearing buffers (Smart clear A+B) and optical clearing buffer (Easy Index).
Easy Clear: allows up to 10 independent samples (in 50mL tubes) to be placed for washing simultaneously, each at a different temperature*. The shaking conditions can be controlled from gentle to more aggressive frequencies. *Temperature range: 30-90degC.
SmartClear II:

Commercial Software Licenses

Unless otherwise stated – latest version is available and supported

Booking is done through Advanced Light Microscopy


2 IA workstations are available at Levine #201 . Spec: Intel Xeon CPU E5-2620 @ 2.0 GHz, 64 GB of memory, NVIDIA Quadro 4000 graphic card. Booking is done through Internal Services => Biomaging Queue.

3 very high performance IA Workstations dedicated to processing of Lightsheet and other very big datasets at Levine #209.

Analysis 30T: 2*Intel Xeon E5-2690 CPU @ 2.6 GHz, 256GB of memory, Nvidia GeForce GTX TITAN X graphic card

Analysis 80T: 2*Intel Xeon E5-2690 CPU @ 2.6 GHz, 256GB of memory, AMD Radeon R9 200 graphic card

Analysis 20T: 2*Intel Xeon E5-2667 CPU @ 3.2 GHz, 512GB of memory, Nvidia Quadro M6000 24 GB graphic card, dedicated fast SSD disk for program cache

Booking is done through Internal Services => Adavanced Light Microscopy.

All the above commercial software are available on the IA workstations, as well as: Fiji, Matlab and selected open-source software (eg. Ilastik, ICY, CellProfiler, Vaa3D). Other open-source software can be installed on demand.

Data storage

In order to enable imaging data backup and availability the cell observatory maintains two types of data servers -

BioImg Server – Central long-term Storage Server for raw imaging data. Automatically collect imaging data from multiple campus wide imaging platforms. Users can document, search, access and share data from anywhere on campus. (BioImg step by step guide)

ESS server - A specially defined large storage with fast communication for data retention analysis and archiving, Supports the large data sets produced by lightsheet microscopes

More info and links to additional training material can be found here.