Synapse Web
	About	Anatomy	Links	Publications	Search	Tools

Will sEM Align run on a Mac?

sEM Align should be compatible with Virtual PC with Windows, a Mac program available from Apple Computer, Inc., that allows you to run PC programs.

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.

How does sEM Align work?

Details on the basic approach and the mathematical computations used by sEM Align can be found in our recent paper:

Fiala JC, Harris KM (2001) Extending unbiased stereology of brain ultrastructure to three-dimensional volumes. Journal of the American Medical Informatics Association. 8(1):1-16. (Preprint 716K PDF)

Why doesn't sEM Align recognize my image files? In the Open Series dialog I can find the folder my images are in, but it doesn't show me the list of images. I can create a new series but I still can't get a list of images using "Goto" from the Section menu.

If you have a set of images that you want to align they'll need to be named in accordance with sEM Align's file naming convention and stored in an acceptable format. Images should be given a name with a leading underscore ('_') and an extension that indicates the section number, e.g. '_mySeries.1', '_mySeries.2'. Acceptable image formats are 8-bit (grayscale) JPEG and Windows Bitmap. The easiest way to get your image files into the correct format and file name convention is to use the Convert file conversion utility. Make sure you explicitly ask Convert to Renumber the Destination files before converting.

OK, I tried renaming my image files to '_mySeries.1', '_mySeries.2', etc. but the Series still is not visible in sEM Align. What's wrong??

If you have manually renamed your images or saved them from another program, make sure that there is not a '.jpg' or '.bmp' extension still on the files. This extension will not always be visible in Windows, since Windows sometimes hides the file extensions of known file types. Once you have images named appropriately you'll see the Series show up in the Open Series dialog.

Can I align color images in sEM Align?

Unfortunately, sEM Align can only handle 8-bit images and expects these images to have a linear color space. So it is not possible to align 24-bit color or 8-bit indexed color images. sEM Align will only align and output 8-bit grayscale images. However, the Convert file conversion utility will take 24-bit or indexed color images in a variety of formats and reduce them to grayscale images for use with sEM Align.

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.

I aligned my images in sEM Align and used "Apply To Images" as above, but they still aren't aligned. Now what's wrong!?!??

Make sure that your series was in absolute alignment. Running "Apply To Images" on an incremental alignment will not produce an aligned series. (If you have no idea what I'm talking about, read the Align help file and the JAMIA paper and start over when you think you understand these.)

If you took the default settings in the "Apply To Images" dialog box, make sure that you are now looking the "aligned" series with IGL Trace, not the original series used for sEM Align.

If you renamed the output in the "Apply To Images" dialog box and used the same name for the series as it was in sEM Align, you may have overwritten your original image files. If this is the case, the original image files are lost forever. But the new images should be aligned when viewed with IGL Trace. The images might not be aligned in sEM Align, however. This would be because sEM Align is using the transforms that are still in the folder, but no longer applicable.

Last Updated: 4/25/02