Zeiss Light Sheet Z1

Our microscopy facility features cutting-edge light sheet fluorescence microscopes from Zeiss. Our goal is to advance the research of the Boston community by offering competitive pricing and expertise.

Application Forms

Zeiss LSM 880

Instrument Snapshot

Light sheet fluorescence microscopes are known for being easy to use and best to use for imaging thin or whole animal samples and long-term imaging of live samples.

Due to the thin, but powerful, sheet of light that this scope has, samples are easily penetrated, providing clear, bright images. Lighting a small section of the sample at once, the Zeiss Light Sheet Z1 also minimizes phototoxicity and photobleaching.

Arivis Vision4D software enables image analysis and rendering.

Reach out to our core facility in Boston with any questions at cils-core@northeastern.edu.



Laser line: 405, 488, 561, 638 nm


Objective: 5×, 10×-water, 20×-CLARITY


CO2/temperature control


Large scale 3D tissue imaging


arivis Vision4D software

Rat Brain Tissue

Treated with a retroviral vector to stain neurons
Instrument: Zeiss Lightsheet Z1
Credit: Shansky Lab

Spinal Cord - Axolotl

Instrument: Zeiss Lightsheet Z1
Stained with 5-ethynyl uridine (EU), RNA synthesizing cells (cyan) and cell nuclei (magenta)
Credit: Jackson Griffiths/Monaghan Lab

African Clawed Frog (Xenopus Laevis) Embryo

Instrument: Zeiss Lightsheet Z1
Expressing green flourescent protein
Credit: Ashwin Lokapally/Sive Lab

Axolotl Limb Regeneration

Instrument: Zeiss Lightsheet Z1
Genetically encoded cell cycle reporter. Magenta: G1 phase cells. Yellow: S/G2/M phase cells
Credit: Eun Kyung Jeon/Monaghan Lab


Internal NU


External Academia






What types of samples can be imaged?

We can do 3D imaging at millimeter-scale. In vivo imaging can be performed on embryos and C. elegans, but for samples larger than embryos, fixation is recommended.

I am not sure how to prepare my sample for imaging. Will I be able to get guidance?

We would be happy to provide guidance on sample preparation prior to imaging. Please reach out to cils-core@northeastern.edu.

How do I mount my samples?

Samples small enough to fit in a capillary (<~1-2 mm in width) and 2 mL syringe (<~2-3 mm in width) can be mounted in 1.5% low melt agarose using the capillary or the syringe respectively. Alternatively, for samples that cannot fit in the syringe, the sample can be superglued onto a 3D printed hook. Depending on the sample size, cutting the sample may be necessary to fit the sample in the imaging chamber. Please reach out to learn about sample mounting for your specific needs.

What media should I image my samples in?

Samples can be imaged in 1x PBS. If you would like to match the refractive index (RI) of the media to the sample to aid in imaging, please reach out to learn about available RI matching solutions and/or if the RI matching solution of your choice can be used at the facility.

How do I clear tissues?
I completed my imaging session. How do I process and analyze the data collected?

We have arivis Vision4D installed on our workstation that can be used for processing and analyzing data. Other opensource software based on needs (ex. FIJI (ImageJ)) are available for use. Please reach out if you would like guidance in data analysis.

Additional Resources

Carl Zeiss Microscopy Online Campus

Education in Microscopy and Digital Imaging

Light-Sheet Fluorescence Microscopy Overview

ZEISS Lightsheet Z.1 Sample Preparation

ZEISS Lightsheet Z.1 Quick Guide:

Imaging with Water or Clearing Immersion

ZEISS Lightsheet Z.1 Quick Guide:

Tile Scanning

Lightsheet Z.1 Operating Manual

Detailed guide to Lightsheet Z.1

Other Instruments

Zeiss LSM 800 (Inverted)

NU user: $35/hr; Academia: $55/hr; Industry: $75/hr

Laser line: 405, 488, 561, 640nm

Objective: 10×20×40×63×

Fixed cell/tissue imaging

Imaging Tiling


Zeiss Axiozoom V16 (Upright)

NU user: $25/hr; Academia: $35/hr; Industry: $50/hr

Continuous zoom with high NA

Large field of view

Apotome.2 Structured Illumination Module

In vivo and model organism imaging

Zeiss LSM 880 NLO (Upright)

NU user: $55/hr; Academia: $75/hr; Industry: $95/hr

Laser line: 405, 458, 488, 514, 561, 594, 640 nm

NIR Laser: tunable line (680-1300 nm); fixed line -1045 nm

Objective: 10×20×20×, 40×20×-CLARITY

Multi-photon imaging

Superresolution (Airyscan)

Spectral Unmixing

Prerequisite: Bioraft Laser Safety Training Part I and II

Our facility

Interdisciplinary Science and Engineering Complex

ISEC 080, 805 Columbus Ave, Boston, MA, 02115