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How to get started at the AOMF

O-MUG

Comprehensive Course on Fluorescence Microscopy


Zeiss AxioScan Fluorescence Whole Slide Scanner


The Zeiss AxioScan is a brightfield and fluorescence slide scanner that digitizes whole tissues sections at high resolution 20x or 40x. For fluorescence, it can image up to 5 fluorophores on one sample with filters covering DAPI, GFP, Cy3, mCherry/TxRed and Cy5 (or similar fluorophores). Images can then be viewed using the free Zeiss ZEN viewer and analyzed using Halo software that we have installed on one of our analysis computer.

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. For fluorescence slide scanning, we suggest booking a short free consultation with one of the AOMF staff to discuss your samples, staining and settings prior to dropping them off for scanning. It is usually a good idea to talk to us even before preparing samples. We can give you tips on sample preparation specifically for the fluorescence scanner. You can also download this document for some tips.

The typical waiting time for scanning, is about 1 week. If you need them sooner, you can opt for our Express Scanning Service. Extra fees will apply and this service will depend on staff availability and the current slide scanning queue. 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 Zeiss ZEN 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). You can download it here.

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 available called (HALO by IndicaLabs, 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 conjunction with all other modules for further tissue class analysis.
  • TMA Analysis - A workflow module for Tissue Microarray 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.

    Download this information sheet to learn more about Halo (AOMF Whole Slide Quantification with Halo.pdf).
Scanner Specifications:
Model
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Zeiss AxioScan (Zeiss Canada) 100 slide capacity

Objective Lenses
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Fluar 2.5x/0.12
Plan-Apochromat 5x/0.16 WD=12.1 M27
Plan-Apochromat 10x/0.45 WD=2.0 M27
Plan-Apochromat 20x/0.8 WD=0.55 M27
Plan-Apochromat 40x/0.95 Corr WD=0.25 M27


Filters
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DAPI (Chroma ET DAPI 49000) GFP (Chroma ET EGFP 49002) CY3/TRITC (Chroma ET CY3/TRITC 49004) mCherry TxRed (Chroma ET mCherry TexasRed 49008) CY5 (Chroma ET CY5 49006)

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

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