Intro: GeoPIXE: Analyzing image regions

Video

Coming soon!

Steps

Analyzing region concentrations

1. Make sure you have the .dai file of interest loaded in the main GeoPIXE window.

2. From the drop-down menu in the main GeoPIXE window, choose the region shape you wish to draw.

3. Click and drag on your image to draw the desired region shape. Most shapes can be adjusted once drawn, and moved around by clicking and dragging on the central dot inside the shape. If you want to remove the region shapes you have drawn, go to Display > Clear all shapes in the main GeoPIXE window.

4. Go to Window > Image Regions to open the Image Regions window.

5. Click on the "Σ" button (can also appear as "S" in some versions of GeoPIXE) below your image. This should populate the Image Regions window with concentrations in your region shape.

6. You can draw more shapes or move the shapes around to analyze more regions. Each set of region concentrations will appear as a new row in the Image Regions window. You can select a row to see the image region shape highlighted on your image.

7. "Delete" will delete the image region row from your Image Regions window. "Clear" will delete all the regions in the Image Regions window.

8. You can save the group of analyzed regions as a .region file by clicking on "Save" in the Image Regions window. You can export the table of concentrations to a .csv file by clicking on "Export" in the Image Regions window.

Extracting region spectra

(NOTE: this will only work if your raw data is also present on the CLASSE server. If your data have been rotated off the disk, you may request that the raw data be restored by submitting a service request ticket to CLASSE IT: https://wiki.classe.cornell.edu/Computing/ServiceRequest)

1. Make sure you have all the regions of interest whose spectra you want to examine analyzed in the Image Regions window.

2. Make sure the drop-down menu next to "EVT" in the Image Regions window is set to "array," not "#0" which is the default.

3. Turn on the cluster option in the Image Regions window if you are connected to the CLASSE cluster.

4. Press the "EVT" button. A window will pop up asking you to save the regions as a .region file. Make sure you choose a location in your analysis directory. Click "Save."

5. Next, you may be asked to navigate to the folder containing your raw data. Go to the correct folder in your raw directory and click "Open."

6. A window will pop up asking you to save the spectra as a .spec file. Make sure you choose a location in your analysis directory. Click "Save."

7. A progress bar should pop up as GeoPIXE analyzes your raw data and extracts the spectra from your selected regions. After a short wait, the spectrum or spectra will load into the Spectrum Display window.

-- LouisaSmieska - 19 May 2016