Morphometrics documentation

Contents

• Create your first project
• Digitizing landmarks on the first specimen
• Single landmarks
• Linear measurements (and scale bars)
• Curves and semilandmarks
• Digitizing landmarks on subsequent specimens
• Move landmarks
• Delete landmarks
• Edit landmarks (rename)

Creating a new project

To create a new project, go to the morphometrics homepage and click the button that says "Create new project". In the box that appears, enter a name, a description (optional), and select whether the project is 2D or 3D.

Once you have created the project, you will be redirected to the overview page for that project. Here you can upload new pictures (for 2D projects) or meshes (for 3D projects). Both media types are currently limited to a maximum size of 10MB. You are also limited to 10MB of space in total (get in touch if you need more space). To start digitizing landmarks, click on the button titled 'Collect landmarks'.

You retain all rights to the images or meshes that you upload. You can delete them at any time. PhyloNimbus will never use your files without your explicit permission.

After collecting landmarks, you can return to this page to dowload them as a .csv file.

 

Digitizing landmarks on the first specimen

The landmark collection page is divided into three parts:

1. The digitization pane - hold the Ctrl key and click in this pane to place a landmark.
2. The landmark pane - the list of landmarks digitized in this project. Click on a landmark in this list to select it (a selected landmark will turn green in the digitization pane).
3. The specimen pane - the list of specimens (pictures or meshes) that you uploaded as part of the project. Click on a specimen to switch to it (you may have to click twice in some browsers).

You can collect three types of measurement: single landmarks, linear measurements (or scale bars), or curves (i.e. semilandmarks). To change which type you collect, click on the respective button above the digitization window. You can collect mutiple types of measurement on each specimen.

Once you create a landmark on one specimen, it will be created (but not placed) for every other specimen in the project.

Collecting single landmarks

Make sure the "Landmark" button is selected. Hold down the "Ctrl" button and left click on the image/mesh. A red landmark should appear on the specimen, and a landmark should appear in the list of landmarks.

Collecting linear measurements/scales

Make sure the "Linear" button is selected. Hold down the "Ctrl" button and left click on the image/mesh twice. A red line should appear between the two points, and the linear measurement should appear in the list of measurements.

To set the length of the measurement (i.e. if it is a scale bar), click on the icon for that measurement. In the box that opens, enter the length of the linear measurement in metres.

Collecting curves/semilandmarks

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.

The number of semilandmarks used to define the curves in 10 by default. This can be changed by clicking the icon on the curve in the landmark list.

Digitizing landmarks on subsequent specimens

Important: Landmarks created on one specimen will be automatically carried over to other specimens.

To switch to another specimen, click on it in the specimen list (3). The existing landmarks should appear in the landmark list, with a red border to indicate that they have not yet been placed.

Click on a landmark that you wish to place, and the border should turn green (this indicates that it is selected). You can now place this landmark on the image or mesh in the normal manner (Ctrl+click).

Moving landmarks

To move a landmark (or curve or linear measurement), select the landmark in the landmark list (2). The border and the landmark will both turn green. Now place the landmark normally (Ctrl+click).

Deleting landmarks

Landmarks can be cleared, which will remove the landmark from the current specimen but keep it in the landmark list, or deleted, which will remove the landmark from every specimen and delete it from the project.

Clear a landmark by clicking the icon next to the landmark. Delete it with the icon.

Editing landmarks

Rename landmarks

Click on the icon on each landmark in the landmark list to give it a new name.