Intro: GeoPIXE: Options for saving images and image data

Image save options

For all options: "Save current" saves the currently displayed elemental map. "Save selected" means you will be able to choose which of the elemental maps to save (convenient for saving many images at once).

• Save elemental map as image: File > Export > Current Image as PNG (no scale or color bars).
• Save all maps at once: File > Save ALL as HTML (PNG). Saves all maps as PNG files in a folder called "html," also saves an html file that can be opened in a browser which shows a preview of all the images.
• Save all maps as black and white images: File > Black and white HTML (PNG). Saves all maps as black-and-white PNG files, also saves an html file that can be opened in a browser which shows a preview of all the images.
• Save elemental map as image with scale and color bars: File > Export > Current Image/Selected Images as CGM or WMF. Other options such as EPS are available through this dialog.
• Save elemental map as tiff with concentration data: File > Export > Selected Images as TIFF > Areal density (ng/cm**2). Should be opened in ImageJ, is not a typical "image" file.
• Save elemental map as ASCII data table: File > Export > Selected Images as ASCII tables > choose delimiter (comma, tab) and whole image or region.
• Save elemental map REGION as concentration table: File > Export > Selected Images as XY conc tables > choose comma or tab delimited.

Multi-element images

• 3-element overlays: Window > 3 Element RGB Images. Choose a different element for each channel. Images can be saved from File > Save as PNG or Save as JPEG.
• Elemental associations: Window > Element Associations. Choose a different element for each channel. Click on the map to draw a spline and edit its shape around a cluster of data points of interest. Right click to remove the spline. Go to Analyze > Within spline to see the selected points highlighted on the main elemental map in neon green. The association plot can be saved at File > Save as PNG in the Associations window. The map with the overlaid green can be saved with File > Export > Current Image as PNG. The green shape can be saved alone with File > Export > Current Assoc. Highlight as PNG > select color.

Viewing images

• I saved images as .png/.jpg files. How do I view them outside of GeoPIXE?
• As mentioned above, GeoPIXE .tiff exports are not typical image files and should be viewed in software such as ImageJ. Documentation here: http://rsb.info.nih.gov/ij/docs/index.html
• You may wish to view exported data tables in Matlab. Matlab is available on the CLASSE compute cluster. Documentation here: https://wiki.classe.cornell.edu/Computing/MatLAB

-- LouisaSmieska - 16 May 2016