Integrated Light Microscopy Core

Histology

Full color imaging for histological stains
Check Microscope StatusNew User Training

Hands-on Microscopes

To access a microscope, click the New User Training button above and work through our training checklist. Trained users have 24/7 access to the facility and are given permission to schedule their own microscope sessions through our online scheduling software.
Zeiss Axioskop upright histology microscope

Overview: This microscope is optimized to meet the needs of those who want high resolution histological work. Data can be captured with the digital camera and analyzed on an analysis station.

Location: KCBD 1250F

Training Contact: Christine Labno

Emission Detection:

  • Brightfield, phase contrast and Nomarski (DIC)
  • Axiocam 14-bit CCD digital color camera (6.7 um pixel size, 1300x1035 pixels)

Objectives:

  • 4x / 0.10 NA
  • 10x / 0.3 NA 5.2mm WD
  • 20x / 0.5 NA 2.0mm WD
  • 40x / 1.3 NA oil 0.21mm WD
  • 100x / 1.3 NA oil 0.2mm WD
  • Also available:
  • 1.25x /0.035 NA
  • 25x / NA oil/glycerol
  • 40x / 0.6 NA or 40x Korr
  • 63x / 1.4 NA oil

Features:

  • QImaging software on Windows 10
  • Upright platform
Zeiss Axiovert 200M inverted widefield microscope - DECOMMISSIONED NOV 2023

This microscope is no longer available for use, it has been replaced with a Zeiss Axio Observer 7.  The information here is for publication generation purposes only.

Click for user's guide

Overview: The Axiovert 200M is a fully motorized, inverted widefield microscope from Zeiss. This microscope is used for immunofluorescence, Nomarksi (DIC) or full color histology images on fixed or live specimens on slides. The high quality images can be further enhanced by digital deconvolution on the analysis stations. Users may capture their images using the ORCA ER digital camera for fluorescent samples or the Zeiss Axiocam color digital camera for samples which require transmitted light color imaging.

Location: This microscope is no longer available for use

Training Contact: N/A

Fluorophores this microscope can image:

  • Blue (e.g. DAPI)
  • Green (e.g. GFP, Alexa 488)
  • Red (e.g. mCherry, Alexa 594)
  • Far Red (e.g. Alexa 647)
  • Full color histology imaging with white light

Emission Detection:

  • Hamamatsu Orca Flash 4.0 camera with 4 megapixels (6.5um pixel size, 2048 x 2048 pixels). Huge field of view, great for tissue samples and multi-well plates
  • Zeiss Axiocam 14-bit CCD digital color camera (6.7um pixel size,1300x1035 pixels)

Objectives:

  • 10x / 0.5 NA
  • 20x / 0.5 NA
  • 40x / 1.3 NA oil
  • 40x Korr
  • 63x / 1.4 NA oil

Sample Chamber:

  • Inverted platform and multiple stages to support slides and dishes for live and fixed samples
  • Automated z-drive for z-stacks
  • Automated xy stage for fine movement
  • Chamber slide users see our chamber slide use warning before starting your cultures!

Special Features:

  • SlideBook software for image capture
  • Automated reflector turret with 5 positions and a multitude of fluorescent filters
  • Automated condenser turret
  • Dual filter wheels with individual excitation filters for fluorescence
  • Nomarksi (DIC) imaging
AxioObserver 7 automated, inverted widefield

Overview: Fully automated AxioObserver 7 widefield microscope with incubation chamber, fluorescence and DIC optics, full color histology, Prior motorized XY stage, and high NA objectives with auto-immersion capabilities at a wide range of magnifications and excellent Axiocam 705 monochrome and Axiocam 305 color CMOS cameras. Zeiss Zen software  (blue edition) with AI automated sample finder, XYZT automation including time lapse, slide scanning, and mark and find multipoint over time capabilities. Fluorescence filters for DAPI, cyan, green, yellow, red, far red, and near IR plus DIC prisms for select objectives.

Location: KCBD 1250F

Training Contact: Lorraine Horwitz

Fluorophores this microscope can image:

  • blue (e.g. DAPI)
  • cyan (e.g. CFP)
  • green (e.g. GFP/Alexa 488)
  • yellow (e.g. YFP)
  • red (e.g. DsRed, mCherry, Alexa 594)
  • far red (e.g. Cy5, Alexa 647)
  • near IR (e.g. cy7)

Excitation Light Source:

  • LED light source

Emission Detection:

  • Monochrome and color CMOS cameras

Objectives:

  • 5x dry
  • 10x dry
  • 20x dry
  • 40x / 1.1 water - rewatering feature
  • 63x / 1.4 oil

Sample Chamber: XYZ automated inverted microscope stage

Drop Off Service

We have two slide scanners that are run purely as a drop-off service.
40x CRi users -- please note that after 13 years of service this scanner has broken beyond our ability to repair. There is no service contact or US distributor. Please choose another scanner for your project!
To use the service: first see our Slide Preparation and Practical Considerations documents.
First-time Core users will need to create an account on the Core data server by logging in to the server terminal (must be done IN PERSON in the KCBD 1250 office) and submit a Facility User Record.
All users need to bring a completed copy of the Scanner Service Request Form and your slides in a container labeled with your name to KCBD 1250
We will add your slides to the queue and email you when your scans are done. Scan files will be available for download on the KCBD Core data server for 30 days. Physical slides should be picked up from designated areas as soon as possible after scanning. Slides not picked up within 3 months become the property of the Core and we will discard them if we run out of storage space.
To view your images: For CRi .mrxs files use CaseViewer (PC only) or QuPath; for Olympus VS200 .vsi files use OlyVIA or QuPath. We have created guides for basic OlyVIA and basic QuPath use
Contact Khalil Rodriguez for more information on this service
Olympus VS200 Slideview Research Slide Scanner

Click for freeOlyVIA software download or free QuPath whole slide image analysis software from the University of Edinburgh

The Core has created a guide for beginning OlyVIA software use (in progress) and a guide for beginning QuPath use with whole slide scans. The QuPath developers have extensive documentation as well.

Click for our Slide Preparation Guidelines and our Practical Considerations for Slide ScanningImage of the Olympus VS200 whole slide scanner and computer work station in KCBD 1250E

Overview: Slide scanning on the Olympus VS200 Slideview is run as a drop off service. Our whole slide scanners create a virtual library of histology or multi-channel fluorescent slides. Details on the virtual slide can then be zoomed to a virtual magnifications from 0.5x-100x and exported as .tif or .jpeg for analysis or presentation with other software packages. We currently recommend processing with either the opensource QuPath software package or the proprietary free download from Olympus called OlyVIA.

Location: KCBD 1250E

Drop off Contact: Khalil Rodriguez

This microscope can image:

  • Full color histology imaging with white light
  • Blue (DAPI) ex 378/52 em 432/36 (Quad dichroic)
  • Cyan (CFP) ex 438/24 em 482/25 (Triple dichroic)
  • Green (FITC, GFP) ex 474/27 em 515/30 (Quad dichroic)
  • Yellow (YFP) ex 509/22 em 544/24 (Triple dichroic)
  • Orange (TRITC) ex 554/23 em 595/31 (Quad dichroic)
  • Red (mCherry) ex 578/21 em 641/75 (Triple dichroic)
  • Far red (Cy5) ex 635/18 em 698/70 (Quad dichroic)
  • Near IR (Cy7) ex 735/28 em 809/100 (Single dichroic)

Excitation Light Sources:

Emission Detection:

Objectives:

  • 2x, 4x, 10x NA 0.4, 20x NA 0.8, and 40x NA0.95 dry
  • 60x NA 1.42 oil (small regions only, file size and scan time can balloon quickly)

Pixel Sizes:

  • 2x - 3.275 um/pixel (fluorescence), 2.7382 um/pixel (histology)
  • 4x- 1.507 um/pixel (fluorescence), 1.3691 um/pixel (histology)
  • 10x - 0.6504 um/pixel (fluorescence), 0.548 um/pixel (histology)
  • 20x- 0.3251 um/pixel (fluorescence), 0.274 um/pixel (histology)
  • 40x - 0.1626 um/pixel (fluorescence), 0.137 um/pixel (histology)
  • 60x - 0.1084 um/pixel (fluorescence), 0.091 um/pixel (histology)

Special Features:

  • Drop off service: drop off your slides and put your name in the queue. We'll do the rest and notify you when your scans are done. Slides are scanned on a first-come, first-served basis.
  • Automated scanning of up to 210 slides per run, unlimited slides per batch
  • Data is available on our server, so you can download it straight to any campus computer.
  • Offline image viewing software available free from Olympus (Windows only) or analysis software free from QuPath at the University of Edinburgh (multi-platform: Windows, MacOS, Linux).
CRi Pannoramic SCAN 40x Whole Slide Scanner - NO LONGER FUNCTIONAL

The 40x CRi scanner has broken down after 13 years of service. There is no service contact and currently no US distributor, so we cannot repair or replace this system. This information is here for legacy purposes ONLY (grant and publication writing with existing scans). Please choose one of our other two scanners for your project.   

Click for free CaseViewer software download or free QuPath whole slide image analysis software from the University of Edinburgh

Click for our Scanner Slide Preparation Guidelines and our Practical Considerations for Slide Scanning

Drop off Contact: No longer in service, please choose a different system

This microscope can image: nothing currently, it is broken and cannot be repaired. Information here is for legacy purposes only.

Emission Detection: Allied Vision Technologies Stingray F146C color, 4.6 um per pixel camera

Objective: 40x NA 0.95 LWD Zeiss objective, virtual magnification range from 0.5x to 100x on high resolution (down to 0.12um/pixel) tiled images

Pixel Sizes: 0.1644 um/pixel (fluorescence) and 0.1645 um/pixel (histology)

Special Features:

  • Drop off service: drop off your slides and put your name in the queue. We'll do the rest and notify you when your scans are done. Slides are scanned on a first-come, first-served basis.
  • Automated scanning of up to 150 slides per batch
  • Data is available on our server, so you can download it straight to any campus computer.
  • Offline image viewing software available free from 3DHistech (Windows only) or analysis software free from QuPath at the University of Edinburgh (multi-platform: Windows, MacOS, Linux).
CRi Pannoramic MIDI 20x Whole Slide Scanner

The CRi scanners are now over a decade old and are no longer supported in terms of repairs, parts or even purchasing a new version of the system (no US distributor). They are starting to malfunction more frequently and while we are currently able to repair them in house, there may come a time when that is not possible.  We will keep them running as long as we are able, but they may die without warning at any time.  We are encouraging existing scanner clients to move their scans to the newer Olympus VS 200 as soon as they are comfortable. We're happy to scan the same slide in both machines so that you may compare scan quality.Click for free CaseViewer software download or free QuPath whole slide image analysis software from the University of Edinburgh

Click for our Slide Preparation Guidelines and our Practical Considerations for Slide Scanning

Overview: Slide scanning on the Pannoramic scanners is run as a drop off service. Our whole slide scanners from Cambrige Research and Instrumentation (CRi, now owned but NOT SUPPORTED by a spinoff of ThermoFisher) create a virtual library of histology or multi-channel fluorescent slides. Using the proprietary software available in the facility or as a free download, details on the virtual slide can then be zoomed to a virtual magnifications from 0.5x-100x and exported as .tif or .jpeg for analysis or presentation with other software packages.

Location: KCBD 1250E

Drop off Contact: Khalil Rodriguez

Fluorophores this microscope can image:

  • Blue (e.g. DAPI)
  • Green (e.g. GFP, Alexa 488)
  • Red (e.g. mCherry, Alexa 594)
  • Far Red (e.g. Alexa 647)
  • Full color histology imaging with white light

Excitation Light Sources:

  • HXP 120 C arclamp with fiber optic lightguide for fluorescence
  • Incandescent white light bulb for histology

Emission Detection:

  • Zeiss AxioCam MRm high sensitivity, 12-bit greyscale, 6.45um per pixel camera for fluorescence imaging
  • CIS 3CCD 3 megapixel color camera for histology

Objective: 20x Zeiss LWD objective, virtual magnification range from 0.5x to 100x

Pixel Sizes: 0.3225 um/pixel (fluorescence) and 0.3225 um/pixel (histology)

Special Features:

  • Drop off service: drop off your slides and put your name in the queue. We'll do the rest and notify you when your scans are done. Slides are scannned on a first-come, first-served basis.
  • Automated scanning of up to 12 slides per batch
  • Data is available on our server, so you can download it straight to any campus computer.
  • Offline image viewing software available free from 3DHistech (Windows only) or analysis software free from QuPath at the University of Edinburgh (multi-platform: Windows, MacOS, Linux).