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Why the name sEM Align?

sEM stands for serial electron microscopy. Alignment of serially-sectioned tissue photographed at the electron microscope is our primary use for the software.

Why do I get an error "Image is too large" when I try to align?

You are trying to use IGL Align by accessing Acquire and Align from the IGL Trace Section menu. IGL Align can only work with small images. You'll want to use sEM Align, which can only be run as a separate program, to align large images.

Is sEM Align as fast as IGL Align, or would I see a significant performance advantage with the 3D board and IGL Align?

sEM Align is probably not as fast as current accelerators but there are other advantages to using it (see below).

In addition to not requiring special purpose hardware, what other advantages does sEM Align have over IGL Align?

• sEM Align can handle large images (whereas the IGL Align could only handle images less than the screen size, e.g. 1024x768)
• sEM Align runs on any Win32 operating system (Win95, 98, NT)
• Additional degrees of freedom can be introduced into the alignments
• A point correspondence feature allows automatic alignment based on a few points input by the user
• Alignment parameters are saved separately from the images so that alignments can be copied, undone, averaged, and adjusted
• sEM Align allows incremental alignments in which a single can be corrected without requiring the whole alignment to be redone

I've aligned my images in sEM Align, but when I open them in IGL Trace they aren't aligned. What's wrong?

sEM Align doesn't alter the images you're aligning, it stores alignment information in separate files. IGL Trace doesn't know how to read this separate information, so there's an extra step to prepare the series for IGL Trace after alignment.

After aligning your images into absolute mode (see Help), use the "Apply to Images" operation from the Series->Transforms menu to generate a new series of aligned image files (that incorporate the separate alignment information). This new series can be opened with IGL Trace as an aligned series.

Note: The "Apply to Images" operation is a little complicated and very slow, so I suggest you try it on only one or two sections at first, and then verify that what you're getting is ok before proceeding with an entire series.

Last Updated: 11/21/00