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


Mild repetitive TBI reduces brain-derived neurotrophic factor (BDNF) in the substantia nigra and hippocampus: A preclinical model for testing BDNF-targeted therapeutics
Wooden Steps to Shallow Depths: A New Bathymodiolin Mussel, Vadumodiolus teredinicola, Inhabits Shipworm Burrows in an Ancient Submarine Forest
Milk Exosomes Anchored with Hydrophilic and Zwitterionic Motifs Enhance Mucus Permeability for Applications in Oral Gene Delivery
Engineered Bacteria Titrate Hydrogen Sulfide and Induce Concentration-Dependent Effects on Host in a Gut Microphysiological System
Endothelial Glycocalyx Sensitivity to Chemical and Mechanical Sub-Endothelial Substrate Properties
Controlling Pericellular Oxygen Tension in Cell Culture Reveals Distinct Breast Cancer Responses to Low Oxygen Tensions
Hypoxia-Inducing Cryogels Uncover Key Cancer-Immune Cell Interactions in An Oxygen-Deficient Tumor Microenvironment
Direct Differentiation of Human Pluripotent Stem Cells into Vascular Network along with Supporting Mural Cells


Bioengineered Perfused Human Brain Microvascular Networks Enhance Neural Progenitor Cell Survival, Neurogenesis, And Maturation
Pten, Pi3K and PtdIns(3,4,5)P3 Dynamics Modulate Pulsatile Actin Branching in Drosophila Retina Morphogenesis
Medioapical Contractile Pulses Coordinated between Cells Regulate Drosophila Eye Morphogenesis
Cationic Carrier Mediated Delivery of Anionic Contrast Agents in Low Doses Enable Enhanced Computed Tomography Imaging of Cartilage for Early Osteoarthritis Diagnosis
Sox17 Mediates Adult Arterial Endothelial Cell Response to Hemodynamics
Cold Exposure Impairs Extracellular Vesicle Swarm–Mediated Nasal Antiviral Immunity
Lineage-Mismatched Mitochondrial Replacement in an Inducible Mitochondrial Depletion Model Effectively Restores the Original Proteomic Landscape of Recipient Cells
Exploring Functional Protein Covariation across Single Cells Using nPOP
Transport of Symbiont-Encoded Cellulases from the Gill to the Gut of Shipworms via the Enigmatic Ducts of Deshayes: A 174-Year Mystery Solved
Click Chemistry-Enabled Conjugation Strategy for Producing Dibenzodiazepinone-Type Fluorescent Probes To Target M2 Acetylcholine Receptors
Developing a Transwell Millifluidic Device for Studying Blood-Brain Barrier Endothelium
Diosmin and Its Glycocalyx Restorative and Anti‐Inflammatory Effects on Injured Blood Vessels
pH-Responsive i-motif-Conjugated Nanoparticles for MRI Analysis
Hybridization Chain Reaction Fluorescence In Situ Hybridization (HCR-FISH) in Ambystoma mexicanum Tissue
Intra-Articular Kinetics of a Cartilage Targeting Cationic PEGylated Protein for Applications in Drug Delivery
Charge-Based Drug Delivery to Cartilage: Hydrophobic and not Electrostatic Interactions are the Dominant Cause of Competitive Binding of Cationic Carriers in Synovial fluid
In vitro Testbed Platform for Evaluating Small Volume Contrast Agents via Magnetic Resonance Imaging
Usability of Deep Learning Pipelines for 3D Nuclei Identification with Stardist and Cellpose
A Long-Circulating Vector for Aptamers Based upon Polyphosphodiester-Backboned Molecular Brushes
Hypoxia Inhibits the Cardiac IK1 Current through SUMO Targeting Kir2.1 Activation by PIP2
Denoising Multiplexed Microscopy Images in N-Dimensional Spectral Space
Cationic Peptide Carriers Enable Long Term Delivery of Insulin-Like Growth Factor-1 to Suppress Osteoarthritis-Induced Matrix Degradation
Increasing the Throughput of Sensitive Proteomics by plexDIA
Targeting Oncogenic KRAS with Molecular Brush-Conjugated Antisense Oligonucleotides


Local Mechanical Stimuli Correlate with Tissue Growth in Axolotl Salamander Joint Morphogenesis
Maximizing TLR9 Activation in Cancer Immunotherapy with Dual-Adjuvanted Spherical Nucleic Acids
Single-Dose Intra-Cartilage Delivery of Kartogenin Using a Cationic Multi-Arm Avidin Nanocarrier Suppresses Cytokine-Induced Osteoarthritis-Related Catabolism
Regenerating Axolotl Retinas Regrow Diverse Cell Types with Modulation by Notch Signaling and Reconnect to the Brain
Wnt Signaling Coordinates the Expression of Limb Patterning Genes During Axolotl Forelimb Development and Regeneration
A Constitutively Expressed Fluorescence Ubiquitination-Based Cell Cycle Indicator (FUCCI) in Axolotls for Studying Tissue Regeneration
Development of Fluorescently Labeled, Functional Type I Collagen Molecules
Interstitial Flow Enhances the Formation, Connectivity, and Function of 3D Brain Microvascular Networks Generated within a Microfluidic Device
Regeneration and Assessment of the Endothelial Glycocalyx To Address Cardiovascular Disease
Mild Repetitive Head Impacts Alter Perivascular Flow in the Midbrain Dopaminergic System in Awake Rats
Quantitative Imaging of Blood-Brain Barrier Permeability Following Repetitive Mild Head Impacts
High-Throughput Microfluidic 3D Biomimetic Model Enabling Quantitative Description of the Human Breast Tumor Microenvironment
Injectable Lignin-co-Gelatin Cryogels with Antioxidant and Antibacterial Properties for Biomedical Applications
Mechanical Causation of Biological Structure: Productive Pulls Produce Persistent Filaments in a Human Fibroblast Model of Matrix Development
Bottlebrush Polymer-Conjugated Melittin Exhibits Enhanced Antitumor Activity and Better Safety Profile
Two-Photon Peak Molecular Brightness Spectra Reveal Long-Wavelength Enhancements of Multiplexed Imaging Depth and Photostability


Stiffening of the Extracellular Matrix is a Sufficient Condition for Airway Hyperreactivity
Biomaterials and Oxygen Join Forces to Shape the Immune Response and Boost COVID-19 Vaccines
Imaging in vivo Acetylcholine Release in the Peripheral Nervous System with a Fluorescent Nanosensor
A DNA-Based MRI Contrast Agent for Quantitative pH Measurement
Confocal Imaging Capacity on a Widefield Microscope Using a Spatial Light Modulator
Lung Injury in Axolotl Salamanders Induces an Organ‐Wide Proliferation Response
3D Visualization of Macromolecule Synthesis
Self-Assembled DNA–PEG Bottlebrushes Enhance Antisense Activity and Pharmacokinetics of Oligonucleotides


High-Power Light-Emitting Diode Array Design and Assembly for Practical Photodynamic Therapy Research
Engineering Bacillus subtilis as a Versatile and Stable Platform for Production of Nanobodies
Optical Nanosensors for in vivo Physiological Chloride Detection for Monitoring Cystic Fibrosis Treatment
Site‐Specific Bioconjugation and Convergent Click Chemistry Enhances Antibody–Chromophore Conjugate Binding Efficiency
Real-Time Particle-by-Particle Detection of Erythrocyte-Camouflaged Microsensor with Extended Circulation Time in the Bloodstream
Multichannel Correlation Improves the Noise Tolerance of Real-Time Hyperspectral Microimage Mosaicking