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Olympus Upright BX51

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Whole Slide Scanning
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How to get started at the AOMF


Comprehensive Course on Fluorescence Microscopy

Aperio Whole Slide Scanner

The ScanScope XT, by Aperio technologies, is
a brightfield scanner that digitizes whole microscope slides at 20x and 40x magnification and provides fantastic high resolution images
(~ 0.5 microns/pixel for 20x and ~ 0.25 microns/pixel for 40x scans). Images can be up to 100,000 by 100, 000 pixels in size (which would result in huge gigabyte files), but they are JPEG2000 compressed to a few hundred megabytes for an average-sized specimen. These images can then be easily viewed with Aperio's free image viewer, called ImageScope, which also allows you to take snapshots and perform quantitative analysis.

Full Service Scanning
We do not offer training for this instrument, but we provide full service scanning at 20x and 40x magnifications. Just bring us your slides, we will scan them and then return them to you along with the digitized images. The typical waiting time for scanning, is about 1 week. If you need your slides scanned sooner, you may request to use our Express Scanning Service. Extra fees will apply. For our slide scanning fees, click here.

If you are interested in this service, please contact us or come by the facility and visit us for more information!

Image Viewing/Analysis Software
Once you get these beautiful scanned images, then you'll most likely want to do something with them. So first thing you'll need is the Aperio ImageScope software to open and view the images. This software is free, easy to use and can be installed on any PC (sorry, not on MACs yet). Click here to download Aperio ImageScope (Version 10).

Most of you will then want to analyze the images in some way. So, for your whole slide image analysis needs, the AOMF also has many Aperio analysis algorithms available for you to use in our facility and we also provide training on all of them.

Here are some of the analysis algorithms available:
  • Positive Pixel Count (this is available free with ImageScope download) - allows for the measurement of area and intensities of up to two stains (Ex. measuring the positive DAB staining).
  • Membrane - detects membrane staining for individual cells and quantifies their intensity and completeness.
  • IHC Nuclear - this algorithm can be used to detect nuclei and quantify their staining intensity.
  • Deconvolution - this algorithm is useful for separating and quantifying area and intensity of multiple stains.
  • Microvessel Analysis - this is used to angiogenesis measurements
  • Rare Event Detection
And for more complex analysis problems...

Aperio Genie Histology Pattern Recognition software:
This very powerful software, allows you to train it to pick up different tissue types based on their patterns (for example, picking up tumour regions). Then you can use the algorithms described above to quantify things like nuclear staining in the tumour regions.

Free Aperio image viewer - Aperio ImageScope (Version 9)
ImageScope Users Guide
Positive Pixel Count Algorithm Users Guide
Genie Users Guide

Scanner Specifications:
Aperio ScanScope XT
120 slide capacity

Objective Lenses
Olympus 20x/0.75NA Plan Fluor
Olympus 40x/0.75NA UPlanFL N

Input Slide Size
1"x3" (scanning region is 2.5x5cm)

Scan Speed
3 minutes for 15mm x 15mm area at 20x

Illumination Source
Stocker Yale 21DC Halogen Illuminator

Aperio Technologies

For fluorescence whole slide scanning, see our Olympus Upright microscope.

Copyright 2006 Advanced Optical Microscopy Facility. All rights reserved.