Integrated Light Microscopy Core

Whole Slide Scanning

Drop off or do your own
Check Microscope StatusNew User Training

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).

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
Caliber I.D. RS-G4 Large Format Laser Scanning Confocal

Overview: The Caliber I.D. RS-G4 is an upright laser scanning confocal microscope with a motorized XY-Z stage and software designed for large format (tiled) images. This system is ideal for high speed, high quality tiling in 2D or 3D and will handle samples up to 120mm x 80mm x 6mm thick.

Location: KCBD 1250F

Training Contact: Shirley Bond

Fluorophores this microscope can image:

  • Blue (DAPI, Alexa 405)
  • Cyan (CFP)
  • Green (GFP, Alexa 488)
  • Yellow (mCitrine, YFP)
  • Orange (Cy3, Alexa 543)
  • Near Red (Texas Red, Alexa 594)
  • Far Red (Cy5, Alexa 647)
  • Near IR (Alexa 700)

Excitation light source(s):

  • Near UV laser at 405nm
  • solid state laser at 488nm
  • solid state laser at 561nm
  • solid state laser at 640nm
  • solid state laser at 785nm

Emission detection:

  • 2 photon multiplier tubes (PMTs) for emission detection
  • Seven band pass filters for emission range selection: 450/70, 520/44, 550/88, 600/52, 630/69, 670/30 and 832/37
  • 16-bit tif or Imaris .ims file output.

Objectives (base magnification, additional optical zoom is possible):

  • Supports dry, oil and water immersion objectives with a wide range of magnifications available (2x - 100x).
  • Objectives must be programmed in prior to use.

Sample Chamber:

  • Upright platform for imaging of slides
  • Imaging in dishes limited, only possible with dipping (coverslip-free) objectives
  • Fast ribbon / strip mosaic scan mode plus conventional tiling mode, both with real time / online stitching

Special Features:

  • 8kHz Resonant-scanning confocal
  • Large mosaic creation up to 120 x 80 mm with high precision scanning stage.
  • Fluorescence and/or reflectance confocal imaging
  • Automated scanning of single, simultaneous pairs or sequential channels.
  • Automated collection of time-lapse, X-Y-Z, multi-stage points, multiple wavelengths and snapshots.
  • 1024 x 1024 pixel resolution