Tools: sEM Align

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Align is a Windows program for aligning grayscale images. Align accepts only 8-bit per pixel Windows Bitmap (.bmp) or grayscale JPEG (.jpg) images as input and produces only 8-bit per pixel Windows Bitmap grayscale output. The output is suitable for use with IGL Trace for making 3D measurements and reconstructions.

Version 1.26b is available for download from this page.

Download Software (216K zip) [Last update: Dec 28, 2001]

Download Example Series (505K zip) [Last update: Jun 1, 1999]

Download Keyboard Overlay (23K PDF) [Last update: Jun 1, 1999]

Printable sEM Align Help (46K pdf) [Last update: Dec 28, 2001]

Answers to Frequently Asked Questions about sEM Align. [Last update: Jan 26, 2001]

Enhancements in version 1.26b:

Added multithreading to Apply To Images operation so it runs in the background.
Apply To Images now scans all sections for width and height parameters.
Apply To Images automatically skips missing sections.
Apply To Images will now output JPEG as well as BMP.
Apply To Images no longer overwrites existing images without asking.
Fixed tab order in dialogs.
Current transforms are saved before starting Apply To Images.

Enhancements in version 1.20b:

Support for grayscale JPEG section image files.
Improved abort operation from Apply to Images.

Bug fixed in version 1.11a:

Crashes sometimes occurred during Open Series, especially when changing drives.

Enhancements in version 1.10a:

Point correspondence method now includes rigid-body (rotation and translation only) alignment.
Arbitrarily many correspondence points can be entered and used for computed alignments.
Correspondence points can be entered into transformed sections.
On-screen display of correspondence points with deletion.
Incremental alignment method with conversion between absolute and incremental transforms.

System Requirements:

Minimum:

Microsoft Windows
100 MHz Pentium PC
8 Mb of free memory
800x600 display with at least 1024 colors

The speed of alignments is dependent on the speed of the computer and size of the on-screen view, so low system performance can be at least partially compensated by reducing the view size. During normal operation, the program keeps two scaled images in memory, and for each maintains an additional image buffer for the on-screen view. The program requires RAM memory sufficient to hold these images. For images scaled to fit the screen this is usually no more than 6 Mb. When Scaling is not used, memory requirements increase to that needed to hold the actual images in memory.

Recommended:

200 MHz Pentium Pro or better
at least 64 Mb of memory
a fast 1024x768 display with 2Mb video memory

Capabilities and Use:

sEM Align facilitates the alignment of grayscale images by allowing on-screen adjustments of image position, orientation, scale, and distortions up to 2nd order. Alignments are made relative to other images in a sequence of images called a series. Each image in a series is referred to as a section, in reference to material obtained by serial sectioning tissue for electron microscopy, (sEM=serial electron microscopy). Thus, each section is an image stored in a separate file. The position of the section in the series is indicated by a numerical extension.

sEM Align is designed to allow on-screen alignment of larger images than is possible through the use of IGL Align and special purpose OpenGL hardware. sEM Align is implemented completely in software which runs on any general purpose PC. This is accomplished by displaying and moving scaled versions of the original images on screen. Speed of movement and display is proportional to the size of the on-screen view.

Section alignments can be made in several ways. Images can be incrementally moved using keyboard input. Alignments can be computed from a set of feature correspondences specified by the user. The resulting section transforms are stored in separate files. Thus, original image data is not modified by sEM Align. Additionally, the program allows the user to make adjustments to the entire series at once or to make adjustments to a separate view transform which gets applied to every image. For more explanation of how sEM Align works, see the 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. (Offprint 727K PDF)

sEM Align can display two sections blended together. This facilitates putting features of two sections in correspondence since features in both sections can be seen while moving one of them. Another useful feature for validating alignments is flickering between two sections. Aligned features do not generate any apparent motion during flickering, while misaligned features generate apparent motion in the direction of the misalignment.

For increased performance, sEM Align normally does not antialias the display of transformed sections. It is not critical to do this during alignments since no changes are being made to the original data anyway. Each time a section is displayed, the transformed section is recomputed from the image data. However, antialiasing can be performed when desired.

sEM Align is used in our laboratory to align serial sections by following this protocol.

Previous Versions:

Version 1.20b (250K zip) [Last update: Apr 27, 2001]

If there are majors problems with the latest version, try this one instead. Version 1.20b may work under older versions of Windows while 1.26b might not due to multithreading.

Last Updated: 12/28/01