Using ImageJ for what tpsDig does, but on a Mac

If I had discovered this months ago, my thesis would probably be in a much better position right now! I’ve been tied to the PC in my office, rather than being able to go home and watch movies or TV shows while I did my digitizing.

The free program ImageJ is useful for all sorts of things, like processing images for analysis and doing measurements on photographs, but it can also record coordinate (x,y) pairs as an output file, which is perfect for digitizing specimen outlines for later Elliptical Fourier Analysis.

I have been using tpsDig by F. James Rohlf for this, and I’ve never seen an alternative mentioned, probably because most of the other software written for geometric morphometrics is written for DOS and Windows.

Enough blabbering, here’s how to do it:
1. Start ImageJ. Open the image you want to outline.
2. Important! Make sure the coordinate system being used is the same as that in tpsDig (tpsDig places the origin in the lower left, ImageJ in the upper left by default). Select Analyze->Set Measurements…->Invert Y Coordinates.
3. Select the “Polygon Selections” tool on the floating toolbar. [If you’re really good, you could also use the “Freehand Selections” tool and get out scads of numbers.]
4. Outline the object by clicking along the edge of the object. When you close, double click to stop the digitization.
5. Choose File->Save As->XY Coordinates and save your file.
6. You’re done!

To get this to be readable by tpsDig and related software, you will obviously have to add the top three lines that describe the file, the number of landmarks, and the number of curves, as well as the name of the image file as the last line in the file. I don’t have a present need for that, but it’s not too hard to write up an R function (or a terminal script) to add lines (interestingly enough, I’ve been using sed to do this in DOS batch files recently rather than the OS X terminal).

UPDATE: Somewhat annoyingly, ImageJ seems to only open JPG files in RGB colors, not in CMYK. I have no idea why. Luckily, this comes at a time when I am only first starting to realize that CMYK is a more standard color choice than RGB, so most of my files are still in RGB.

If scaling is a factor (it is for me), you can install the Zoom_Exact plugin (near the bottom of the page). Installing this was interesting, but the documentation helped somewhat. What you want to do is:
1. Choose Plugins->New…,
2. Select type “Plugin” and name it “Zoom_Exact”
3. Paste the code into the boz that appears and save it as “Zoom_Exact.java”
4. Restart ImageJ. “Zoom Exact” should appear at the bottom of the Plugins menu.
5. To easily use Zoom Exact, you can map it to a shortcut key with Plugins->Shortcut->Create Shortcut. I have mine mapped to capital “Z” so I can call it up easily when I want to get the scaling right on the screen.

1 thought on “Using ImageJ for what tpsDig does, but on a Mac”

  1. Installing a plugin for ImageJ is much easier than what you describe:

    1. Download the Zoom_Exact.java
    2. Place the file in ImageJ’s plugins directory or a subdirectory (only one level deep max)
    3. Select the menu item “Plugins – Compile and Run”, choose that file, and the plugin is both compiled and run.
    4. If the Plugins menu doesn’t have the “Zoom Exact” entry, run “Help – Update Menus”. (depends on how old your ImageJ ij.jar is).
    Cheers, albert.rierol.net

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