Collect semilandmarks in PhyloNimbus

20th October 2016 by PhyloNimbus

The most update to Phylonimbus brings the ability to collect semilandmarks from both 2D images and 3D meshes.

How to collect semilandmarks

From the documentation:

Make sure the "Curves" button is selected. Hold down the "Ctrl" button and left click on the image/mesh at points that define the curve. Double click at the final point to finish the curve. A red line should appear as you digitize the curve, and the curve should appear in the list of measurements after you have finished drawing it.

Other news

With this update, the PhyloNimbus morphometrics digitization software moves from Alpha to Beta. All the major features that I plan to add are now in place, and future updates will focus on bugfixes and minor improvements. Please get in touch if you have any suggestions.


3D geometric morphometrics now accepts STL files

6th June 2016 by PhyloNimbus

I'm happy to announce that you can now upload STL meshes to 3D projects in the morphometrics app.

The other accepted format for 3D meshes is PLY. Both file formats work equally well in binary or ascii encoding. However, binary meshes take up a lot less space - so if you're running out of free space on the PhyloNimbus server, you might find it worthwhile to convert future meshes to binary files.

How can you tell if a mesh is saved in a binary format?

Just try opening it up in a text editor (e.g. Notepad). If you see rows of numbers, then you have an ASCII file. But if you get lines of gobbledegook and strange characters, then you've got a binary file.

Happy landmark digitizing!

P.S. Meshlab is a free program that will convert meshes between ASCII and binary.


Geometric morphometrics app in alpha release

2nd June 2016 by PhyloNimbus

The PhyloNimbus geometric morphometrics app is currently in an alpha release. It is currently able to collect 2D and 3D geometric morphometric landmarks and linear measurements. We are in the process of adding additional features, in particular for the digitization of semilandmarks.

While in this phase of active development, the software will be in a state of flux. Although we don't anticipate removing any features, we cannot guarantee that new updates will be 100% compatible with earlier versions.

Current features

  • 2D landmark digitization from .jpg files
  • 3D landmark digitization from .ply files
  • Linear measurement in 2D and 3D
  • Scale measurements and landmarks to a scale bar within the image/model

In development

  • Semilandmark digitization
  • Procrustes alignment
  • Landmark statistical analyses

Is the morphometrics software working for you? Is something not working? Do you want to request a feature? Get in touch and let us know.