Guide to the „Unbend specimens‟ module in tpsUtil

Travis C. Haas, Tulane University, New Orleans

thaas@tulane.edu
Version 1.2, 31 March 2011

Introduction

Some fish tend to curve when they die – especially when by suffocation. The „Unbend specimens‟ module in
Jim Rohlf‟s tpsUtil (Rohlf, 2008; available at http://life.bio.sunysb.edu/morph) was created to adjust for that
curvature. If bending is present but not statistically removed prior to shape analyses, spurious findings may
result.

The „Unbend specimens‟ module works by using additional points placed along the backbone or midline of
each specimen to fit a quadratic curve that is used to remove the effect of curvature from all landmarks
(including your original landmarks for shape analysis). For further details on the computations underlying the
procedure, see the „Unbend specimens‟ section of the tpsUtil help file.

A word of warning – if the bending of the specimens in question doesn‟t fit the shape of a quadratic curve,
using „Unbend specimens‟ may introduce spurious variation in landmarks. For an alternative to the unbending
procedure utilized by the „Unbend specimens‟ module, see Valentin et al. (2008), which presents a more general
method of dealing with bent specimens. To help you decide if use of the „Unbend specimens‟ module is
appropriate for your specimens, you can assess the fit of a specimen‟s curvature to a quadratic curve by
examining the R2 value provided by „Unbend specimens‟ (for further details, see page three of this document).

Preparing data files

Before using „Unbend specimens,‟ all specimens should first be digitized (i.e., landmarks for shape analysis
placed on all images and saved in a .tps file). For further details on the use of Jim Rohlf‟s tps suite
(http://life.bio.sunysb.edu/morph/) for digitizing specimens, see pages 1-4 of Heidi Schutz and Jonathan
Krieger‟s excellent guide at:
http://www.morpho tools.net/softwareguide/GM%20guide%20v4%20LMs.pdf

Next, choose four or more points that will be used to fit the quadratic curve that will adjust for curvature. These
points can include existing landmarks for shape analysis, as well as additional points (landmarks or sliding
semilandmarks) that you add along the midline. The additional points can be deleted from the dataset once an
appropriate unbending has been achieved for the shape analysis landmarks.

Use tpsDig to add these additional landmarks to each specimen in your existing .tps landmarks file. See below
for an example:

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I had originally placed 11 landmarks (shown as red dots) on each specimen for shape analysis:

To these I added an additional four points (indicated with solid arrows in the image below) to be used for the
„Unbend function‟: the fork of the tail, plus three others along the midline. In total, I used five points to perform
the unbend; the fifth point was provided by an existing shape analysis landmark (the tip of the snout, indicated
with a dashed arrow in the image below).

Save the new .tps file that now includes your original shape analysis landmarks as well the additional landmarks
added to be used in performing the „Unbend specimens‟ procedure. This is the only .tps file that will be used in
the remainder of the unbend procedure.

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Finally, you will need to create a curve points .nts file that lists the landmarks from your new .tps file that will
be used to define the curve. An example is shown below. In my example, five landmarks (12, 13, 14, 15, and 3)
were chosen with which to define the curve. The first and last points should define the two ends of the curve
(left to right). The order of the other points does not matter. The second number in the second row (in this case a
“5”) indicates the total number of landmarks to be used to define the curve.

" 3k backbone file

1 5 1 0
12
13
14
15
3

The .nts file can be created by opening a new Notepad document, copying and pasting the text shown above,
adjusting the text to reflect your specific set of landmarks, then selecting 'Save As' and adding .nts to the end of
your file name instead of the default .txt.

You are now ready to implement the „Unbend specimens‟ procedure in tpsUtil.

Implementing ‘Unbend specimens’ in tpsUtil

Open tpsUtil. Under „Operations‟, select „Unbend specimens‟.

In the „Input file‟ box, single click the „Input‟ button. Select your .tps file that includes all shape landmarks as
well as landmarks that will be used to perform the unbend operation.

In the „Output file‟ box, single click the „Output‟ button. Select a location and name for the new file that will be
created after unbending is performed. This new file will include the “unbent” landmarks versions of all of your
specimens in .tps format.

In the „Actions‟ box, single click the „Setup‟ button. In the new „Unbend specimens‟ window that will appear,
single click the „Curve pts.‟ button in the „Actions‟ box. Open the .nts file that lists the landmark numbers that
you wish to be used to perform the unbending operation. Click the „Unbend‟ button. You can click on the up
and down buttons in the „Preview‟ box to view the adjustments made to each specimen as a result of the unbend
function, as well as the R2 value for each. The R2 value should be consulted to determine if the bending of a
given specimen fits the shape of a quadratic curve. If the R2 value is particularly low, you may choose to instead
utilize alternative methods for unbending (see, e.g., Valentin et al. (2008)). Finally click „Create‟ to create a
new .tps file (already named and located in the folder you chose earlier) containing your unbent specimens.

If you don‟t want to use the added landmarks in subsequent shape analyses, you can remove them from the
unbent specimens file by taking the following steps in tpsUtil: From the „Operation‟ box, select „Delete/reorder
landmarks‟. From the „Input file‟ box, click „Input‟, then open your unbent specimens .tps file. Click the
„Output‟ button on the „Output‟ file box. Choose a name and location for the new .tps file that will be created;
this .tps file will contain only the landmarks you choose to retain in the next step.

In the „Actions‟ box, click „Setup‟. In the new „Delete landmarks‟ window that appears, uncheck any landmarks
you wish to delete from your file, i.e., all landmarks that were used only for unbending and which you don‟t
wish to use in your shape analyses.

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Click „Create‟ in the „Actions‟ box. The newly created file (with the name and location you chose earlier),
which includes “unbent” landmark coordinates for all specimens, may now be used for whatever shape analyses
you choose to implement.

Acknowledgements

Thanks to Stephen Jacquemin and Carmelo Fruciano for providing useful suggestions that improved the
document.

Literature cited

Rohlf, F.J. 2008. tpsUtil, file utility program. version 1.40. Department of Ecology and Evolution, State
University of New York at Stony Brook.

Valentin, A.E., X. Penin, J.-P. Chanut, J.-M. Sévigny, and F.J. Rohlf. 2008. Arching effect on fish body shape
in geometric morphometric studies. Journal of Fish Biology 73: 623–638.