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Quick Start

Get from a fresh install to your first analysis in about ten minutes. For the full picture, see the User Guide.

1. Install

Download the package for your platform from the releases page and install it — see Installation for the details and the exact file names.

Launch Modan2 from the Start Menu (Windows), Applications (macOS), or by running the AppImage (Linux).

2. Create a dataset

  1. Click “New Dataset” (Ctrl+N)

  2. Give it a Dataset Name and set the Dimension to 2D or 3D

  3. Click Save

The dataset appears in the tree on the left. (Importing a landmark file creates its own dataset, so for that you can go straight to the next step.)

3. Get your data in

If you already have landmark coordinates:

  1. Click Import (Ctrl+I), then Open File, and pick the file — the format is detected from the extension (TPS, NTS, X1Y1, Morphologika, or a JSON+ZIP package)

  2. Check the Dataset Name — the import creates a new dataset — and click Execute Import

The new dataset appears in the tree with its objects. You can also drag a landmark file onto the dataset tree, which opens the same dialog with the file chosen.

If you are starting from photographs:

Select a 2D dataset and drag the image files onto the object table — each image becomes an object named after its file. Digitize them in the next step.

4. Digitize landmarks

  1. Double-click the first object in the table to open it — Landmark mode is active by default

  2. Click on the image to place landmarks; they are numbered in order

  3. Zoom with the mouse wheel, pan by right-dragging empty space

  4. Drag a landmark to move it, right-click it to delete it

  5. Click Save, then use Next / Previous to work through the dataset

Tip

To capture an outline rather than discrete points, switch to Curve mode and trace it — the trace snaps to image edges and is resampled into evenly-spaced semi-landmarks. See Semi-landmark Curves.

If a landmark cannot be placed on a specimen, mark it missing rather than skipping it, so every object keeps the same landmark count — see Handling Missing Landmarks.

5. Add variables (optional)

Variables are what CVA and MANOVA group by. Without any, an analysis computes PCA only.

  1. Open the dataset dialog → Variables tab → “Add Variable”, and name it (e.g. Species)

  2. Open each object and fill in its value for that variable

6. Run the analysis

One run computes PCA, CVA, and MANOVA together — there is no analysis type to choose.

  1. Select the dataset and click Analyze (Ctrl+G)

  2. Set the superimposition method (Procrustes is the default) and the CVA and MANOVA grouping variables

  3. Click OK

7. Explore the results

Open the finished analysis in the Data Exploration dialog to get an interactive scatter plot — PC1 vs PC2 by default, coloured by group, with other axis combinations, a regression overlay, and a shape grid available.

To export, select the dataset and choose Export (Ctrl+E) for the data, or use Export Chart in the Data Exploration dialog to save a plot.

Typical workflow

1. Create a dataset
     ↓
2. Import data (landmark files, or images to digitize)
     ↓
3. Digitize landmarks / trace curves
     ↓
4. Add variables (optional, for grouping)
     ↓
5. Analyze  (superimposition → PCA + CVA + MANOVA)
     ↓
6. Explore and export

Essential shortcuts

Shortcut

Action

Ctrl+N

New dataset

Ctrl+Shift+N

New object

Ctrl+Shift+O

Edit object

Ctrl+I

Import

Ctrl+E

Export

Ctrl+G

Analyze

Ctrl+S

Save changes

Quick fixes

Imported objects do not appear

Click the dataset in the tree to refresh it.

Clicking does not place a landmark

Check that you opened the object dialog and that the Landmark mode button is selected — not Curve or Calibration.

Analysis fails

The dataset needs at least 5 digitized objects, and every object needs the same number of landmarks; mark gaps as missing rather than leaving objects short. See Troubleshooting Guide.

Next steps