ACSII II Guide to Geometric Morphometrics in MorphoJ
2. Preparation
The input to MorphoJ analysis is a data file that can be text (.txt), from Rohlf’s statistical package (.tps), or NTSPC format (.nts). The final output of MorphoJ analysis is a set of statistical results and visualizations. But as we can see from the flow chart above, there are several steps involved before starting an analysis with MorphoJ.
In this user guide, we shall put the digital images in a dedicated folder and show each step with examples and explanations.
1. Digital Image: Take digital images and put all the images in a designated common folder. Download tpsutil and tpsDIG2 from The Morphometrics at SUNY Stony Brook website (http://life.bio.sunysb.edu/morph/).
2. Digitize: Build tps file
a. Open tpsutil.
b. From ‘Select operation’ choose ‘build tpsfile from images’
c. Click input, find your images and click any image from this folder
d. Click output, Create a name for the tps file that will be created.
e. Click setup actions window. All images are checked, uncheck any that you don’t want in the file ‘Include’.
f. Make sure that ‘Include path’ is unchecked. This will include only the image name in the tps file. This is helpful if digitizing file will be saved in the same folder as images, and will result in a short name for the images.
g. Click ‘Create’ and the tps file is ready to be digitized.
3. Digitize Images using tpsdig:.
a. Choose: File>Input source>File and select the tps file you created.
b. First image should appear (may take a few moments). Explore all tabs, find out how to zoom in and out, Delete a specimen, Set scale, Mark landmarks or outlines, change size and color of symbols and labels.
For each images you need to
1. Set the scale:
a. Options>Image tools (or hammer icon). The last tab is ‘Measure’
b. Click set scale, measure ruler, change Reference length and units if needed, click OK.
2. Digitize landmarks
a. Change size or color of dot: Image tools, the first tab is ‘Color’.
b. Label landmarks: In options – Label landmarks (or # icon).Change size and color of number if desired in Tools>Color.
3. Save file. When you save the file choose: File>save data>Overwrite. It is important to choose ‘Overwrite’ instead of ‘Append’. Use ‘Append’ if you want to combine two different datasets (this can also be done with tpsutil.
4. Examine tps file with text-reading software if desired.
A landmark file with 18 landmarks created using tpsdig will look like this:
LM=18
11.00000 173.00000
26.00000 131.00000
47.00000 122.00000
………………………
………………………
18 rows
IMAGE= Lythrurus_Lateral. 211L.JPG
ID=0
SCALE=0.17
In tpsDig the digitized file could be saves as .tps or .NTS
The following link also gives a brief overview of how to place landmarks in digital images.
http://www.morpho-tools.net/softwareguide/GM%20guide%20v4%20OLs.pdf
