Data acquisition

These programs are used to digitized landmark locations, capture outlines, or to interface with devices such as digital calipers. See the utility webpage for programs to manipulate data files and transform file formats.

Note: all of the software in the tps---- series listed below are freely available for use in research and teaching.

Digitize landmarks & outlines from image files, scanner, or video. Windows. TpsDig is a Windows (rough 11) program for digitizing landmarks and outlines for geometric morphometric analyses. Includes simple image enhancement operations, scale factors, image brightness profile, and support for AVI and MOV files. Output is in the TPS file format used by the "tps series" of programs. The TPS file includes the name of the image file for each specimen so that landmarks can always be visualized on the image. Because output files are plain ASCII they can be edited to convertd to formats for other software. Users should note that the tpsUtil program is useful for both the preparation of the input files to tpsDig as well as for some useful conversions afterwards. The program also computes areas of enclosed regions, perimeters, and linear distances. The tpsDig2 link at the left is for the 2.32 version.

There are now some helpful guides and tutorials available on the web:

• tpsUtil & tpsDig tutorial.
• 1. Building a TPS file from Images using tpsUtil.
• 2. Digitizing Morphological Landmarks using tpsDig.
• IINTRODUCCION A TPSdig.avi.
• Collecting Landmarks (PDF)

The tpsDig1 link is for the previous version (1.40 dated 1/17/04). Execute the downloaded file to install the program. By F. James Rohlf.

The old Win 3.1 version is also still available (Version 1.07 dated 4/4/97).

Collect geometric morphometric landmarks in your browser. PhyloNimbus is a web app for collecting 2D and 3D landmarks, linear measurements, and curves/semilandmarks. Coordinates can be downloaded in different file formats. It runs in all major browsers and is compatible with Windows, Mac and Linux. By Dominic.

Morphometrics in Medical Entomology – Collection of Landmark for Identification and Characterization. Versions for Linux (midnight- or gnome-commander), Windows (32 and 64 bits), and Apple (Yosemite). By J-P. Dujardin.

StereoMorph is an R package with tools for the collection of 2D and 3D landmark and curve data. StereoMorph includes a browser-based digitizing application, functions for automatically calibrating a set of two or more standard digital cameras using a simple checkerboard, and functions for reconstructing, aligning, and unifying 3D landmark and curve sets. Complete tutorial and example projects (2D and 3D) can be found at the current URL listed on the CRAN page. MAC/Windows/Linux. Compatible with most web browsers, including Chrome, Firefox, and Safari. By Aaron Olsen and Annat Haber.

A utility to downsample curves stored in TPS files to sets of equal numbers of points (or will-be semilandmarks). For Windows. Link. Developed by Eladio Marquez. Version 1.0.

Landmark was developed by the scientists at the Institute for Data Analysis and Visualization (IDAV) and the University of California, Davis. Working together with collaborators at the American Museum of Natural History, the team was able to build an easy to use tool for 3D landmark editing and placement on geometric surfaces typically obtained via laser range scans.). Version 3.6. Documentation, and software as well as an example of its application to "evolutionary morphing.". Version 3.6.

The developer now has a commercial version (Checkpoint) that has additional features. See https://www.stratovan.com/products/checkpoint.

COO 2D images manual digitization of landmarks I, II or III (+ semilandmarks). readme, from http://mome-clic.com/wp-content/clic-package/coo_start.txt JP. Dujardin, http://mome-clic.com/clic-package

CooRecorder

CBeeWing