Advanced Analytical Centre Resources How to view/edit element maps from Jeol 8200 EPMA

How to view/edit element maps from Jeol 8200 EPMA

Procedures for extracting single element image files from mapping on the JXA 8200

Downloaded data from element mapping includes:

1. A file named 0.cnd which is a text file (opened by any text editor) that includes all the conditions for the mapping (such as number of elements mapped and by what technique, spot size, step size and pixel dimensions of maps).

2. A separate file for each element mapped named in the style (number).(element).pm (eg. This is another text file that is used in the JEOL software to create a thumbnail picture, not much use except it tells you which number map refers to what element (although they are listed in order in the 0.cnd file too). The * file refers to the backscatter/secondary electron image collected along with the element data.

3. A separate binary data (image) file for each element named in the style (number).map.z  In this case the number corresponds to the number used in file type 2 listed above. (e.g. as in the example in 2. above, a binary data file named  is for Mg). This is a zipped (compressed) file.

To extract the separate images for each element:

Unzip each of the *.map.z files. (using winzip or the like). This will give you a file named (number).map, this is a binary data file containing the raw intensities collected for the relevant element at each pixel.

To view/edit unzipped element maps

To edit/view the *.map file using a program capable of extracting binary image files (like the freeware program ImageJ – alternatively the more recent versions of Adobe Photoshop should be able to open these files directly).

In ImageJ use File-Import (rather than Open). Choose the actual *.map file….and hit OPEN. In the import options choose “raw” and set Image type to “16-bit Unsigned”, input the width and height of the map in pixels (this data is in the 0.cnd file mentioned above) – offset = 0, slices = 1 and gap between images 0.