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StereoInvestigator Overview

StereoInvestigator is a powerful stereology software package which can take you from simple point counting to mind bending analysis of your images. Which is a good thing as there is a great deal more to images than meets the eye. It can be used in a two dimensional mode to estimate the frequency of say cell types, collatingthem into categories and performing appropriate statistical analysis. It can also be used in three dimensional analysis, focussing through a thick section and marking the change in cell frequency through the planes of focus.

Stereology is a method where 'walk before you can run' is a good rule of thumb. It ranges from simple techniques to highly specialised analytical methods. If you are uncertain how to proceed, it is strongly advised you obtain advice from someone experienced in the technique. Do this before you begin your investigation - not half way through. It's easy to collect numbers, quite another to collect reliable ones.

Below are pdf files of the entire users' manual (not really a good read to start with, unless you're an experienced user seeking an advanced technique) and selected chapters to get you started.

Click on the pdf icons below to download the appropriate file.
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StereoInvestigator Software Manual


This is most of the instruction manual as provided by the manufacturer, it contains a lot of information, so if you intend to read through it be prepared to spend some time doing it.

You may find it easier to target specific chapters and become familiar with bite sized chucks of the software as appropriate to your needs. Individual chapters have been posted below with a brief description of their contents.
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Chapter 5: Moving Around StereoInvestigator


How the joystick interacts with the navigation and measurement of your sample. Aligning a specimen, moving automatically to a new region as you move beyond the field of view. Essentially, the basics of moving about to examine your specimen and set up where to analyse.
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Chapter 6: Contours and Tracing


Tracing around your area of interest, modifying your trace, deleting, etc. Describes various features associated with a trace such as luminance, brightness, perimeter, area and the overall shape of the region.
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Chapter 7: Markers


What markers are used for and how to assign them to features of interest. Editing marker types and positions and working with marker combinations to label more complex relationships.
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Chapter 8: Automating Image Acquisition


Be prepared to do a bit more thinking undertaking the tasks described in this chapter. Automated tasks can save you a great deal of time, but usually require a time commitment to learn how to use them in the first place. It's something of a balancing act between doing a number of boring repetitive tasks by hand and being finished, or potentially, spending the same amount of time automating it. Your call.
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Chapter 9: Image Stacks


In this context, 'image stacks' refers to the type collected (usually) using a confocal microscope. Features, such as neurones, can be traced through the 3D volume defined in the z series of images taken one above the other through a range of focus planes. The focus slices are already aligned when imported into StereoInvestigator.
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Chapter 10: Serial Sections


Similar to Chapter 9, except this chapter describes how to analyse serial sections which have been physically cut and are also in need of alignment to recreate an accurate 3D volume for analysis.