AMCF IMAGING TECHNOLOGIES
SUPER-RESOLUTION TO MICROSCOPIC TO MESOSCOPIC IMAGING
- ZEISS ELYRA PS.1 SUPER RESOLUTION MICROSCOPE
- ZEISS LSM 800 WITH AIRYSCAN FOR HIGH RESOLUTION IMAGING
- ZEISS 710 CONFOCAL LASER SCANNING MICROSCOPE
- ZEISS CELLDISCOVERER 7
- ZEISS AXIOSCAN 7 WHOLE SLIDE IMAGING SYSTEM
- MILTENYI BIOTEC ULTRAMICROSCOPE II LIGHT SHEET FLUORESCENCE MICROSCOPE
- X CLARITY TISSUE CLEARING SYSTEM
- HALO-EQUIPPED WORKSTATION
- IMARIS-EQUIPPED WORKSTATION
*Adapted from Miltenyi Biotec
ZEISS ELYRA PS.1 SUPER RESOLUTION MICROSCOPE
The Zeiss ELYRA PS.1 is an inverted microscope designed for super-resolution (SR) structured illumination microscopy (SIM) and single-molecule localization microscopy (SMLM) including Photo Activated Localization Microscopy (PALM) using photo-switchable/convertible fluorescent proteins, Total Internal Reflection Fluorescence (TIRF) and STochastic Optical Reconstruction Microscopy (STORM) using specific fluorescent organic dyes. 
The Elyra S.1 can image four fluorescent colors, roughly corresponding to DAPI, Alexa488/GFP, RFP/Alexa568, and CY5/A647 (see below) during SIM imaging, PALM/STORM imaging can capture 2 channels. SIM uses structured light patterns to excite and collect (traditional fluorophores) in small areas that are rotated and accumulated over time to generate a composite SR image. PALM/STORM requires specific photo-activated/photo-converted/blinking fluorophores (see
Maximum Resolution
- Structured Illumination Microscopy (SIM) ~120 nm (x, y), ~300 nm (z), ~15 um (z range)
- Single-molecule localization microscopy (SMLM)
Excitation
- 405 nm, 488 nm, 561 nm, 640 nm
Emission
- DAPI; BP 420-480 nm
- GFP/A488; BP 495-550 nm
- RFP/A568; BP 570-620 nm
- A647/CY5; LP 655 nm
- DAPI + GFP + Cy5; BP 420-480/BP 495-550/LP 650 nm
Objectives (NA, immersion medium, coverslip correction [mm], working distance [mm])
- Plan-Neo 10x (0.3, air, 0.17, 5.2)
- Plan-Apo 63x (1.4, oil, 0.17, 0.19) for SIM
- Alpha Plan-Apo 100x (1.46, oil, 0.17, 0.11) for SIM, TIRF, PALM/STORM
System Overview
- Zen Black software
- Axio Observer.Z1 for Superresolution
- SR imaging achieves resolutions two times better than traditional confocal microscopy.
- In general, SR is not fast imaging. Multiple images must be collected and processed to achieve SR imaging.
- SIM can image to depths of 10-15 microns into a sample using common, robust fluorophores (up to four at one time).
- PALM/STORM requires specific fluorophores/dyes, possibly imaging buffers to capture fluorescent signals in up to two channels at one time.
- Workstations that are HALO-equipped or IMARIS-equipped are available to reconstruct/analyze images.
Educational Resources
- SR imaging requires specialized sample preparation. Read the Elyra Sample Prep Guide and review the educational webinar with Zeiss (below) for more information.
- Visit the AMCF Imaging Resources page for information regarding parameters for successful SIM, TIRF, PALM/STORM imaging, and for Data Sharing and Management plans.
- Watch our recent Super Resolution Workshops with Zeiss (10/2022)
- Single-Molecule Localization Microscopy: Theoretical Basis and Practical Guide
- Additional educational modules are available for AMCF researchers. Contact the AMCF staff to request access.
- Visit our Resources and Grant Planning pages for more information, including acknowledgement use, reproducibility/rigor standards, and Data Sharing and Management plan resources.
ZEISS LSM 800 WITH AIRYSCAN FOR HIGH RESOLUTION IMAGING
The Zeiss 800 CLSM with Airyscan is an inverted microscope with transmitted (HAL), UV (HBO) and laser excitation for collection transmitted light images (brightfield and DIC) and/or confocal fluorescence images. This system dramatically increases conventional confocal image resolution to ~180 nm using Airyscan technology distributing light across an array of detectors (see link in system highlights). Fast linear scanning and high-sensitivity GaAsP detectors increase the imaging speed and sensitivity for most imaging applications including, multi-channel, co-localization, live cell, 3D, and time series imaging. Enhanced sensitivity supports use of lower laser powers to reduce photobleaching and phototoxicity during live cell imaging. Contact the AMCF to learn more and/or schedule your reservation. Reference figure, Korobchevskaya et al. 2017.
Maximum Resolution
- Non-Airyscan ~250 nm
- Airyscan (63x only) ~180 nm
Excitation
- 405 nm, 488 nm, 561 nm, 640 nm laser lines
- Nomarski optics for overlayed transmitted and fluorescent light images
Emission
- DAPI/Hoechst/A350; BP 420-470 nm, associated dye list
- GFP/A488; BP 515-565 nm, associated dye list
- A555/dTom/TRITC; BP 575-640 nm, associated dye list
- 34 channel spectral imaging
Objective type (NA, immersion medium, coverslip correction [mm], working distance [mm])
- EC Plan-Neo 10x (0.03, air, 0.17, 5.2)
- Plan-Apo 20x (0.8, air, 0.17, 0.55)
- LD C-Apo 40x (1.1, water, 0.17, long distance)
- Plan-Apo 40x (1.3, oil, 0.17, 0.21)
- Plan-Apo 63x (1.4, oil, 0.17, 0.19) for airyscan use
System Highlights
- Zen Blue software
- Axio Observer.Z1
- Definitive focus; optimal/automatic (re)focusing during long-term imaging
- Airyscan (w/ 63x obj) provides resolutions above traditional confocal microscopy (~1.7-fold increase in x-y plane to provide ~180 nm resolution)
- 2 GaAsP-PMTs for enhanced imaging sensitivity
- Automated x-, y-, z-axis motors for automated imaging
- Incubator with temperature, CO2, O2, and humidity control for live cell studies
- ROI bleach, 3D imaging (z-stacks) with orthogonal presentation, co-localization, time-series and FRAP
- Workstations that are HALO-equipped or IMARIS-equipped are available to reconstruct/analyze samples
Educational Resources
- Basic Principles of Airyscan Detection (Zeiss, PDF)
- ZEISS Webinar: LSM 800 with Airyscan (YouTube)
- Airyscan Acquisition and Processing step-by-step (Video, settings review)
- Visit our Resources and Grant Planning pages for more information, including acknowledgement use, reproducibility/rigor standards, and Data Sharing and Management plan resources.
ZEISS 710 CONFOCAL LASER SCANNING MICROSCOPE
The Zeiss 710 LSM is an inverted microscope with transmitted (HAL), UV (HBO) and laser excitation to collect transmitted light images (bright field and DIC) and/or confocal fluorescence images. This system supports most basic imaging applications, multi-channel and spectral, co-localization, live cell, 3D, and time series imaging. Contact the AMCF to learn more and/or schedule your reservation. Fluorescent image, Muthuraj et al. 2021.
Maximum Resolution
- ~250 nm
Excitation
- 405 nm, 458 nm, 488 nm, 514 nm, 561 nm, 633 nm
- Nomarski optics: overlayed transmitted and fluorescent light images
Emission
- DAPI/Hoechst/A350; BP 420-470 nm, associated dye list
- GFP/A488; BP 500-550 nm, associated dye list
- Cy3/A555/dTom/TRITC; BP 575-640 nm, associated dye list
- 34 channel spectral imaging
Objectives
Objective type (NA, immersion medium, coverslip correction [mm], working distance [mm])
- EC Plan_Neo 10x (0.03, air, 0.17, 5.2)
- Plan-Apo 20x (0.8, air, 0.17, 0.55)
- EC Plan-Neo 40x (1.3, oil, 1.7, 0.21)
- Plan-Apo 63x (1.4, oil, 1.7, 0.19)
- DIC Slider 10x, 20x, 40x, 63x
System Highlights
- Zen Black software
- Axio Observer Z1
- Definitive focus; optimal/automatic (re)focusing during long-term imaging.
- Automated x-, y-, z-axis motors for automated imaging.
- Extra-large incubator with temperature, CO2, O2, humidity control for live cell studies.
- ROI bleach, lambda scan (spectral imaging) with linear unmixing module.
- 3D imaging (z-stacks) with orthogonal presentation, co-localization, time-series, spectral or channel-based FRET and FRAP.
- Workstations that are HALO-equipped or IMARIS-equipped are available to reconstruct/analyze samples
Educational Resources
- Overview of key functions, imaging configurations for Zeiss 710 (AU BioImaging, start at 20 min)
- Introduction to spectral imaging and linear unmixing (Zeiss, Learning Portal)
- Introduction to spectral unmixing (Zeiss, video tutorial)
- Setting up lambda scan/spectral imaging on Zeiss 710 (video tutorial)
- FRET: Scanning parameters for acceptor photobleaching FRET (apFRET)
- Photobleaching: Scanning parameters for FRAP
- Visit our Resources and Grant Planning pages for more information, including acknowledgement use, reproducibility/rigor standards, and Data Sharing and Management plan resources.
ZEISS CELLDISCOVERER 7
The Zeiss Celldiscoverer 7 is a widefield imaging system for automated, time-lapse imaging of live samples. Samples may be imaged on slides, dishes, and across an array of multi-well dishes including 96 well plates. The system offers a temperature and C02 controlled incubation system for optimal short- and long-term live sample imaging. ZEN Blue allows users to calibrate the system to their sample carrier, input exact imaging parameters, and create a focus strategy keeping the sample in focus across locations and timepoints. While widefield imaging offers accelerated imaging of larger views of view at lower resolutions when compared to confocal microscopy, this system is equipped with afocal magnification changers for high resolution imaging of smaller fields of view that can be subsequently stitched together to generate larger field of view composite images. Contact the AMCF to learn more and/or schedule your reservation.
Maximum Resolution
- ~250 nm
Excitation
- 385 nm, 470 nm, 567 nm, 625 nm
Emission
- DAPI/GFP/RFP/A660
- BP 410-440 nm/500-530 nm/580-605 nm/660-760 nm, associated dye list
Objectives
Objective type (NA, immersion medium, coverslip correction [mm], working distance [mm])
- Plan-Apo 5x (0.35, air, NA, NA)
- Plan-Apo 20x (0.7, air, automated coverslip correction, 2.2)
- Plan-Apo 50x (1.2, water, auto-immersion, automated coverslip correction, 0.84)
* Automated correction for glass/cycloolefin bottom thickness (0.13-0.21 mm) and polystyrol bottom thickness (0.15-1.2 mm).
System Highlights
- Zeiss Zen 2.3 Celldiscoverer software
- Axioscan 506 monochrome camera.
- 20x afocal magnification changer provides 10x/0.35, 20x/0.70, 40x/0.7 imaging.
- 50x afocal magnification changer provides 25x/1.2, 50x/1.2, 100x/1.2 imaging.
- Automatic and customized focusing options with heated objectives.
- Incubator with temperature, CO2, O2, and humidity control for live cell studies.
- Tiling, fast acquisition, image analysis, multichannel, z-stack, time series, movie recorder, experiment designer.
- Workstations that are HALO-equipped or IMARIS-equipped are available to reconstruct/analyze samples
Educational Resources
- Overview of system features (video)
- Visit our Resources and Grant Planning pages for more information, including acknowledgement use, reproducibility/rigor standards, and Data Sharing and Management plan resources.
ZEISS AXIOSCAN 7 WHOLE SLIDE IMAGING SYSTEM
The Zeiss Axioscan 7 is a high-performance whole slide scanning system for fluorescence and brightfield/transmitted light imaging. Up to 100 slides can be imaged using customized scanning profiles using a specialized slide cassette system allowing slides to remain upright and untouched during the imaging process. Fluorescence and brightfield imaging modes are independent. Resulting images can be combined in the data analysis core to maximize data collected from your samples. This system supports traditional IF and IHC imaging as well as cyclic immunofluorescence. Representative images scanned at AMCF (top: H&E breast tissue, bottom: murine brain with DAPI, A568, A647, Katy Emanuel). Researchers must complete Whole Slide Imaging (WSI) sample submission form prior to submitting samples for imaging. Contact the AMCF to learn more and/or schedule your reservation.
Maximum Resolution
- ~250 nm
Excitation Lines
- 385 nm, 430 nm, 475 nm, 511 nm, 555 nm, 590 nm, 630 nm, 735 nm
Emission
- CFP/YFP/mCherry;
- BP 406-440 nm/494-528 nm/ 583-600 nm, associated dyes list
- DAPI/GFP/Cy3.5/Cy7
- BP 375-395 nm/455-483 nm/583-600 nm/720-750 nm, associated dyes list
- DAPI/GFP/Cy3/Cy5/Cy7
- BP 370-400 nm/450-488 nm/540-570 nm/614-647 nm/720-750 nm, associated dyes list
Objectives
Objective type (NA, immersion medium, coverslip correction [mm], working distance [mm])
- 5x (slide overview image)
- Plan-Apo 10x (0.45, air, 0.17, 2.0)
- Plan-Apo 20x (0.8, air, 0.17, 0.55)
- Plan-Apo 40x (0.95, air, 0.17, 0.25)
System Highlights
- ZEN Blue 3.5 Slidescan software
- Axioscan 7 KMAT Microscope
- Axiocam 705 color camera (Sony IMX250 Exmor CMOS).
- Axiocam 712 mono camera (Sony IMX304 Exmor CMOS).
- Available high- and low-magnification focus maps with automated and/or custom/modifiable focus points.
- Modular slide trays/cassettes for contactless slide imaging.
- This system is only operated by AMCF imaging specialists.
- Contact Tissue Sciences Facility for help preparing samples for your multiplexed/cyclic immunofluorescence study and Axioscan 7 imaging.
- Workstations that are HALO-equipped are available to analyze samples
Educational Resources
- Researchers must complete Whole Slide Imaging (WSI) sample submission form prior to submitting samples for imaging.
- In the notes section, indicate reference locations for setting collection parameters for individual channels within/across slides, if needed.
- Watch our recent Educational Webinar (12/2022) on whole slide image analyses using HALO
- Whole-Slide Image Analysis and Quantitative Pathology with QuPath (available in AMCF core)
- Visit our Resources and Grant Planning pages for more information, including acknowledgement use, reproducibility/rigor standards, and Data Sharing and Management plan resources.
MILTENYI BIOTEC ULTRAMICROSCOPE II LIGHT SHEET FLUORESCENCE MICROSCOPE
Tissues are inherently three dimensional in nature, which makes imaging intact tissues a necessity for a more complete study in the relationship between structure and function and the system-level study of cellular mechanisms. With the Miltenyi Biotec (previously La Vision) Ultramicroscope II Light Sheet fluorescence microscope (LSFM) you can extend your existing fluorescent imaging into true 3D, large-scale volumetric imaging of intact tissues and small organs/organisms. Unlike traditional laser scanning microscopy using parallel/identical excitation and collection paths, LSFM excites your sample in an orthogonal beam path. By setting the width, numerical aperture (NA), and Rayleigh length of illumination, users can optimize the shape of the light sheets for their specific sample size and imaging goals. A lower NA results in a broad field of view at the expense of a lower z-resolution and vice versa, with a full range of gradations in between. Using this approach LSFM can reduce out of focus light, capture larger fields of view and collect volumetric images 10’s to 100’s of times faster than traditional confocal microscopes. Optimized volumetric imaging requires removal of light bending cellular components (mostly lipids) through a process called optical clearing. See section below for automated tissue clearing in the AMCF. Light travels differently in different imaging media. The UltraMicroscope II’s onboard software allows users to choose between various preloaded clearing and imaging solutions to optimize imaging. Representative image from AMCF, metastatic tumors in murine lung, Dr. Grinu Matthews. Contact the AMCF to learn more and/or schedule your reservation.
Maximum Resolution
- ≥ 2 um (x, y), ≥ 5 um (z)
Excitation
- 488 nm, 515 nm, 561 nm, 636 nm, 787 nm
Emission
- GFP/Alexa 488, Rhodamine Red, Mitotracker Red, Cy3, TRITC, DsRed, mCherry, Cy5, TO-PRO3, DyLight 633, Alexa 633, Alexa 790 and DyLight 800
- BP 500-550 nm, 520-550 nm, 575-615 nm, 590-650nm, 653-708 nm, 818-873 nm
Objectives
Objective type (NA, immersion medium, coverslip correction [mm], working distance [mm])
- MI Plan 1.1x (0.1, DC40 [1.33-1.49] DC57 [1.50-1.57], 16-17 mm)
- MI Plan 4x (0.35, DC 33 [1.33-1.41] DC49 [1.42-1.48] DC57 [1.50-1.57], 15-16 mm)
- MI Plan 12x (0.53, DC 33 [1.33-1.41] DC49 [1.42-1.48] DC57 [1.50-1.57], 8.5-10.9 mm)
System Highlights
- 1x, 1.6x, 2.5x intermediate magnification optics
- Multiple sample holders
- Flat top, spiked, clamp with closed or open bottom.
- Samples (~ 1.5 cm x 1.5 cm x 1.5 cm) are placed on sample mounts for imaging.
- Researchers may use an available dissection microscope to mount samples for imaging, see below.
- Two imaging chambers/cuvettes are available: X-Clarity/Aqueous (RI 1.46), Ethyl Cinnamate (ECi, RI 1.56)
- The system must be (re)calibrated when chambers/cuvettes are changed.
- Workstations that are IMARIS-equipped are available to reconstruct/analyze samples
Educational Resources
- Overview and Applications for Light-Sheet Microscopy (UNC, Pablo Ariel) Overview of LSFM, tissue clearing, and imaging on the UltraMicroscope II system.
- UltraMicroscope II Users Guide (UNC, Pablo Ariel) Provides critical information regarding sample preparation, imaging parameters and expectations.
- Watch on-demand Miltenyi Biotec training courses to learn more about sample preparation, imaging logistics, and to view some representative studies.
- Samples must be secured (spiked holder, or super glued) sample base for imaging. Small samples (i.e. zebrafish) should be embedded in 0.5 - 2% low temperature melting agarose (Sigma Aldrich A9414) prior to mounting/imaging. Consult with AMCF prior to scheduling your imaging session.
- Researchers should minimize sample sizes to facilitate successful tissue clearing and efficiently manage resultant volumetric image file sizes (10’s to 100’s of GBs).
- Imspector software on the ultramicroscope performs limited visualization, see AMCF’s working with images post LSFM imaging document.
- LSFM is relatively low-resolution imaging in large volumes, higher resolution (≥ 0.25 um x,y, ≥ 0.5 um z) can be obtained in the Multiphoton Intravital & Tissue Imaging Core.
- Learn more about Logos Biosystems DeepLabel antibody staining kits for LSFM imaging. Depending on demand, AMCF will purchase supplies in bulk to offer discounted pricing to individual research groups.
- Logos X-Clarity mounting solution with representative labeling protocol.
- Visit our Resources and Grant Planning pages for more information, including acknowledgement use, reproducibility/rigor standards, and Data Sharing and Management plan resources.
X CLARITY TISSUE CLEARING SYSTEM
To support your volumetric imaging studies, the AMCF also offers equipment for rapid, optimized tissue clearing using the X-Clarity System. Tissue clearing is important for 3D imaging of tissues at single-cell resolutions. The X-CLARITY™ system simplifies and accelerates each step of the tissue clearing process using CLARITY (Clear Lipid-exchanged Acrylamide-hybridized Rigid Imaging / Immunostaining /in situ-hybridization-compatible Tissue hYdrogel), a tissue clearing method developed by the Deisseroth lab at Stanford. Fixed tissues are embedded in a hydrogel matrix and lipids are actively extracted through electrophoresis to create a stable and optically transparent tissue-hydrogel hybrid that is chemically accessible for multiple rounds of antibody labeling and imaging. Native cytoarchitecture remains intact and endogenous fluorescence proteins are preserved for robust fluorescence imaging downstream. For LSFM imaging, samples should be optically cleared (X-clarity), labeled with antibodies, then equilibrated in refractive index (RI) matched mounting solutions prior to imaging. Reference image (right) murine brain optically cleared (X-Clarity) at AMCF.
System Highlights
- This system is only operated by AMCF staff
- Depending on sample size, 1-6 samples may be cleared during each clearing session (< 2.5 cm for 6-well clearing).
Educational Resources
- Reference protocols for tissue clearing/processing using the X-Clarity System
- General (multi-organ, includes Antibody reference list); X-CLARITY Full Protocol and X-CLARITY_General Protocol
- Bone-specific; Greenbaum et al 2017 and X-CLARITY_BONE_Harvard
- Brain-specific; X-CLARITY_BRAIN_Harvard
- Overview and Applications for Light-Sheet Microscopy (UNC, Pablo Ariel) Overview of LSFM, tissue clearing, and imaging.
- X-Clarity is a de-lipidation process, dense tissues with low lipid content may not become completely transparent.
- Cleared samples may be stored in PBS (will cause some temporary whitening) post clearing but must be fully infiltrated in refractive index matching media (RIM) > 24h prior to imaging.
- Logos X-Clarity mounting solution (RIM) with representative labeling protocol.
- Researchers should minimize sample sizes to facilitate successful tissue clearing and efficiently manage resultant volumetric image file sizes (10’s to 100’s of GBs).
- Learn more about Logos Biosystems DeepLabel antibody staining kits for LSFM imaging. Depending on demand, AMCF will purchase supplies in bulk to offer discounted pricing to individual research groups.
- Visit our Resources and Grant Planning pages for more information, including acknowledgement use, reproducibility/rigor standards, and Data Sharing and Management plan resources.
HALO-EQUIPPED WORKSTATION
Maximize your imaging data sets using the premier image analysis platform, HALO (Indica Labs), to perform your quantitative tissue analyses. HALO reports morphological and multiplexed expression data on a cell-by-cell basis across entire tissue sections and maintains an interactive link between cell data and cell image. Click on any cell in the image and immediately see analysis outputs for that specific cell. Sorting and filtering capabilities allow the user to mine millions of cells while visually assessing corresponding cell populations. For example, sort cells according to biomarker intensity and immediately locate cells with highest intensity in the image. The AMCF has several HALO modules ready for use on the HALO image analysis workstation. Contact the AMCF to request permission to independently reserve/use workstations (RSS) and obtain card access for this area. Please see our terms of use agreement for the data analysis workroom.
Overview
- Detailed, quantitative image analysis options for 2D images with full technical support through 2024.
- Located in the Data Analysis Room (DRC I RM 1036, image right)
- Contact AMCF staff to request permission to independently reserve/use workstations (RSS) and obtain card access for this area. Please see our terms of use agreement for the data analysis workroom.
- Simultaneous analysis of an unlimited number of fluorescent markers in any cellular compartment – nucleus, cytoplasm, and/or membrane with the option to define specific cell phenotypes according to marker positivity.
- Analysis tools to identify proximity and relative spatial distribution of objects, cells, and/or features across single tissues or serial sections. This module can be used with any cell-based analysis modules for brightfield or fluorescence.
- Nearest neighbor, proximity, and infiltration analyses, density heatmaps
- Measure any number of fluorescently labeled DNA/RNA ISH probes and immunofluorescent (IF) protein biomarkers on a cell-by-cell basis to rapidly contextualize the corresponding protein and gene expression profile of every cell across the tissue.
Educational Resources
- Learn more about 2D image analysis HALO modules available in the AMCF
- Spatial Analysis, FISH-IF, Highplex Fluorescence, Serial Registration Analysis, Tissue Classifier
- Watch our recent Educational Webinar (12/2022) on whole slide image analyses using HALO
- Visit HALO’s online learning portal (free access with UNMC email registration) to access user guides, technical documents, video tutorials, and webinars.
- Try a free online demo with HALO, simply upload 1-3 images and await your results.
- Visit our Resources and Grant Planning pages for more information, including acknowledgement use, reproducibility/rigor standards, and Data Sharing and Management plan resources.
IMARIS-EQUIPPED WORKSTATION
IMARIS is the world’s leading Interactive Microscopy Image Analysis software focused on 3D and 4D imaging. The AMCF is equipped with the complete IMARIS for Core Facilities software package with focused image analysis, segmentation, and reconstruction options for cancer and neuroscience researchers, cell and developmental biologists. IMARIS can be used for any number of imaging studies but is anticipated to be particularly relevant for researchers using the Elyra PS1 super-resolution microscope and Ultramicroscope II light sheet fluorescence microscopes. Contact the AMCF to request permission to independently reserve/use workstations (RSS) and obtain card access for this area. Reference images, Left; Dr. Grinu Matthew, metastatic lung tumors, Right; super-resolution image, Casey et al. 2021.
Overview
- Detailed, quantitative image analysis options for 3D images with full technical support through 2025.
- IMARIS is well-suited for multiple analyses and sample reconstructions of super-resolution or light sheet fluorescence microscope images.
- Located in the Data Analysis Room (DRC I RM 1036)
- Contact AMCF staff to request permission to independently reserve/use workstations (RSS) and obtain card access for this area. Please see our terms of use agreement for the data analysis workroom.
Educational Resources
- IMARIS offers several research focused applications (visualization and quantification), including educational resources for studies focused on
- Visit IMARIS homeschool to find a diverse array of training videos/tutorials.
- Review the IMARIS User Manual
- Imaris Viewer is a free 3D/4D microscopy image viewer for viewing raw images. Share images, take your high performance Imaris renderings wherever you go. Imaris Viewer works with over 40 microscopy file types, including Tiff.
- Visit our Resources and Grant Planning pages for more information, including acknowledgement use, reproducibility/rigor standards, and Data Sharing and Management plan resources.