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How to get started at the AOMF

O-MUG

Comprehensive Course on Fluorescence Microscopy


Whole Slide Scanner

The ScanScope AT2 is
a brightfield scanner that digitizes whole histology or pathology 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). The images can be easily viewed with a free image viewer, called ImageScope, which also allows you to take snapshots and add annotations.


Full Service Scanning
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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
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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.

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 a program called HALO available, which has a set of analysis modules that you can use in our facility. We also provide training on all of them.

Here are some of the analysis modules available:
  • Area Quantification (IHC & FL) - Separates up to three stains/fluorophores and calculates area, percentage area and intensity/OD. It also calculates colocalization of the stains/fluorophores.
  • Cytonuclear - Quantifies the expression of up to two IHC markers or up to three immunofluorescence (IF) markers in the cytoplasm and/or nucleus.
  • Multiplex/High Plex FL - Quantifies expression of up to four IHC markers or up to eight immunofluorescence (IF) markers in the cytoplasm, nucleus and/or membrane.
  • Tissue Classifier - Identifies multiple tissue classes using a learn-by-example approach based on colour and texture. Can be used in conjuntion with all other modules for futher tissue class analysis.
  • TMA Analysis - A workflow module for Tissue Microaaray organization, analysis and manual scoring. Can be used in conjunction with all other modules.
  • Object Colocalization - Counts objects and measures the area and stain intensity for each object. The algorithm can measure one it two objects (with different stains) and can quantify colocalization of the two objects.
  • Serial Section Analysis - Registers serial sections and allows for regions of interest to be chosen on one slide and then applied to other serial to quantify other markers. Can be used with the Tissue Classifier module as well as other brightfield modules.

Downloads
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Free image viewer - Aperio ImageScope

Scanner Specifications:
Model
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Aperio AT2 (Leica Biosystems)
400 slide capacity

Objective Lenses
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20x/0.75NA UPlanSApo

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

Illumination Source
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LED light source

Links
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Leica Biosystems
HALO


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