RRC-RHTIC: Aperio Training

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Contents

Description

The Aperio System is a whole slide brightfield scanner for 1" x 3" standard microscope slides including whole sections, biopsies and TMAs. The Aperio can scan slides at either 20x or 40x magnification. We are currently investigating 5x and 10x options also. The RHTIC has an image server with the Aperio Spectrum product which can organize image files into projects and allow for batching of image analysis tasks. Within Spectrum there is a tissue microarray (TMA) module called "TMA Lab" which can segment each TMA core into an image. Using TMA Lab you can navigate from core to core within a TMA and input manual scoring data. TMA Lab can be used to display multiple markers for the same TMA spot. It also allows the researcher to run image analysis algorithms on all segmented cores on a TMA and export the data for these analyses into standard CSV files. The image analysis algorithms included with the Aperio System are:

Aperio Image Analysis Algorithms
Algorithm Name Description
Positive Pixel Count Basic pixel classification into intensity bins (0, 1, 2, 3+). Can be used for cytoplasmic markers
Nuclear Finds Nuclei and classifies them as negative, weak, moderate or strongly stained. Used on nuclear markers.
Colocalization Separates up to 3 staining components (e.g. Sirius red and fast green) that are present on the slide and classifies every pixel as being present or absent in each color channel. Works best with 2 color channels. Works for nuclear and cytoplasmic markers.
Microvessel Identifies stained blood vessels and counts their number. Also gives basic size and vessel wall thickness histograms. Works on markers that specifically stain blood vessels.
Micromet A rare event algorithm that detects micrometastasis of tumor cells found in circulating blood.
Membrane Classifies membrane staining into intensity categories. Works on markers that cleanly stain cell membranes.
Genie A genetic self-learning algorithm that is used to automate classification of tissue into component types (epithelium, stroma, blank slide etc...) The previous algorithms can be run within a class found by Genie. Can be run on any marker.


The application needed to view images scanned on the Aperio is ImageScope. It can be downloaded here. You can use ImageScope to extract regions of interest from your images for use in publications and presentations. An example image for installation testing is available here.

If you have images on the Spectrum server and have an account, they can be accessed here: http://aperio.path.uic.edu. When accessing you may receive a certificate error message. We are currently using a self-signed certificate, so click to continue to this web page. We will shortly be installing an external certificate. The first time you access the site you may need to install several browser plugins and/or active X controls.


For frequent users of the facility training on the Aperio system is available. To arrange for training on the Aperio please contact Ryan Deaton at 312-355-4338 or rdeaton@uic.edu.


Aperio Scanning Training

If you need to scan slides you must complete a course on ScanScope and Image Viewing. Training usually takes between 1 and 2 hours to complete. Before coming to the training you need to review the following material and print item 'k':

a. ScanScope User Basics
b. ScanScope Advanced Scanning
c. Image Viewing with ImageScope
d. Remove a Label
e. ImageScope User Guide
f. Digital Slide Studio
g. Turn Off Label Capture
h. -optional-Image Viewing with WebScope-optional-
i. -optional-ScanScope CS Manual-optional-
j. -optional-WebScope User Guide-optional-
k -Documents Used on Training Day-


Aperio Spectrum Training

Spectrum is an online database that tracks slides in research projects. Spectrum is also used to complete image analysis, TMA and Genie related tasks. Scanning training is a prerequisite for Spectrum training. Spectrum training usually takes between 1 and 2 hours to complete. Items a-c below should be reviewed before training. Item 'd.' should be printed and brought with you to training.

a. Spectrum Plus Overview
b. Spectrum Plus User Basics
c. Spectrum Plus Data Management
d. Documents Used on Training Day

Aperio Image Analysis Training

Image analysis is the process of generating meaningful data from images. This training covers the various image analysis algorithms that are part of the Aperio Algorithm Framework. Both Scanning and Spectrum training are prerequisites for this course. This training can take from 1-3 hours to complete. Items a-i are reference material you may need for your analyses. The Image Analysis Seminar Powerpoint file has a lot of very useful information regarding the specific algorithms and their settings. Please print and bring item 'k.' with you to training.

a. Image Analysis 101
b. Image Analysis User's Guide
c. Image Analysis Seminar
d. Color Deconvolution Algorithm
e. Membrane Algorithm
f. Nuclear Algorithm
g. Micrometastasis Algorithm
h. Colocalization Algorithm
i. Microvessel Algorithm
j. Remove a Label
k. Documents Used on Training Day

Aperio TMA Lab Training

TMA Lab is a Spectrum add-on module that allows for the parsing of tissue microarray images into individual cores. Once this is done, you can navigate between cores and view the same core on different slides on the same screen. It also allows for rapid quantification of IHC and other stains and automatically organizes the data by block, sector, row and column. Scanning, Spectrum and Image Analysis trainings are prerequisites for this course. This training will take approximately 1 hour to complete. Please review items a-c. Print and bring item 'd.' with you for training.

a. TMA Lab
b. TMA Lab User's Guide
c. Digital Slide Studio
d. Documents Used on Training Day


Aperio Genie Training

Genie stands for ‘GENetic Imagery Exploration’ and was developed for use in remote viewing applications. It is an add-on module to Spectrum that allows a user to draw representative samples of various tissue classes (blank slide, stroma and epithelium for example) and tell the computer to derive an image analysis algorithm to distinguish novel instances of these classes and apply it to whole slides. For Aperio image analysis users this has the effect of greatly reducing or eliminating the need to draw regions of interest on their images for processing. Scanning, Spectrum, and Image Analysis trainings are prerequisites for taking Genie training. Genie also can tie up the scoring queue for extended periods of time, so Genie training submissions need to be coordinated with the RHTIC. Care needs to be taken in setting up Genie algorithms to avoid extremely long processing times and high charges. This training will take between 1 and 2 hours to complete. Please review items a and b before training. Print item 'c.' and bring it with you to training.

a. Genie
b. Genie User's Guide
c. Documents Used on Training Day
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