Integrated Light Microscopy Core

Histology

Full color imaging for histological stains
Check Microscope StatusNew User Training

Hands-on Microscopes

To access a microscope, contact the Technical Director listed in the description and schedule a hands-on training session. 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: Shirley Bond

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

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: KCBD 1250F

Training Contact: Shirley Bond

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

Drop Off Service

We have three slide scanners that are run purely as a drop-off service.
To use the service, first see our Slide Preparation and Practical Considerations documents, then bring a completed copy of the CRI Scanner Form or the Olympus VS200 Scanner Form and your slides to KCBD 1250.
Contact Shirley Bond for more information on this service.
Olympus VS200 Slideview Research Slide Scanner - NEW Spring 2021

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 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: Shirley Bond or Christine Labno

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 (mCherry) ex 578/21 em 641/75 (Triple dichroic)
  • Red (TRITC) ex 554/23 em 595/31 (Quad 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

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

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 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: Shirley Bond

This microscope can image: Full color histology imaging with white light

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

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 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: Shirley Bond

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).