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Introduction

In addition to alignment by beam scanning the JEOL 9500 system also has a 2D alignment feature. The working principle of this is that the system will take a SEM image of a specified location and compare the SEM image to a reference image. By comparison of these the system will determine an offset and use this for alignment.

Possible advantages of this is

Alignment can be done using either the Secondary Electron or the Back Scatter detector or a combination of them
Alignment might be possible to features with very low contrast
Alignment can be done to an arbitrary shape

The following will illustrate how to set this up. It is a bit more complicated than regular beam scan alignment and knowledge of beam scan alignment is a prerequisite for understanding the following. Please contact us if you would like to try this alignment mode rather than trying on your own. For reference, the JEOL provided manual for 2D alignment can be found here: File:2D mark detecting 20171212.pdf

Reference images

During alignment the system will take SEM images and compare these to reference images of the alignment marks. These reference images can in principle be SEM images obtained from the system but it is simpler to use black and white drawings of the alignment marks. In this example we will use a cross as illustrated below.

Alignment mark used in this example. The mark is 1000 µm in both directions.

The system must know the scale of the mark it is looking for, hence one must assign a physical dimension to the reference mark. The reference image must also be converted to a TIFF image. Both dimension assignment and conversion to TIFF is done with a command in a terminal window. In this example the actual mark is 1000 x 1000 µm and the input image is a PNG file called "PQRef1000mu.png". The command is: ebimg setsize inputimage.png outputimage.tiff dimension

The dimension is given in nanometer. In the example the actual command is ebimg setsize PQRef1000mu.png PQRef1000mu.tiff 1000000

This will generate a TIFF file with a scale of 1000 µm. Next, this must be converted with yet another command to a .ref.gz file. The command is ebimg mkref inputimage.tiff outputimage.ref.gz

In our case it will be ebimg mkref PQRef1000mu.tiff PQRef1000mu.ref.gz

This will generate the actual reference image file with the correct scaling. This file should be moved to


Imagescans obtained during alignment. Rough alignment scan (left) is 1000 µm while fine scan (right) is 10 µm. The green cross indicates the center as determined by the system.