AutoMorph

Community-scale morphometrics provides an remarkable opportunity to quantify the ecological and evolutionary dynamics of taxa in space and time.

AutoMorph is the suite of tools that we have developed to do high-throughput morphometrics on assemblages of objects imaged on a black background. The software (download below) was designed to work with image stacks (each taken at a different focal depth), but also works on individual images as well as photographs.

We developed this approach for extracting 3D shapes from foraminifera imaged with light microscopy, but have also applied it to other fossils (teeth, ostrocods, pteropods, shells) and objects.

Note, our approach current relies on two commercial software packages (Matlab and Zerene Stacker) both of which can be used in ‘trial’ mode if you’d like to try out our image processing routines.

Download software, tutorials, and example images and image products here and on our GitHub site (https://github.com/HullLab):

Software Basic Processing	Includes image segmenting and 2D focusing (extended depth of field) in two functions (segment and focus). Follow instructions on GitHub site to install. To check your installation, you will need to download the example image stack (below).
Software 2D Outline & Measures	One function (run2dmorph) to identify object 2D outline (including coordinates), and basic 2D measures including area and aspect ratio. Code available on GitHub site with instructions for use.
Tutorial Warning: Outdated	Tutorials for all AutoMorph software, including an introduction to the basics of working in your terminal (for Mac Users).
Tutorial Warning: Outdated	Tutorials for all AutoMorph software, including an introduction to the basics of working in your terminal (or command line, for you PC users). This tutorial is targeted at Hull Lab users who will be working remotely on our server, Tide.
Image Stack (Example)	An unprocessed image stack of the sort AutoMorph is designed to work with. Use this image stack to test your local installation.
Segment Output (Example)	Example output (four objects) from ‘segment’ of the example image stack.
Focus Output (Example)	Example output after applying ‘focus’ to the four example objects from segmenting the image stack.
2D Output (Example)	Example output from ‘run2dmorph’ of the four example images after ‘segment’ and ‘focus’.
3D Output (Example)	See recent publication of Hsiang et al (2016), for example output and strengths and weaknesses of the method.

For example, at one North Atlantic site we have imaged the microfossil community in four slides, each accessioned to the Yale Peabody Museum, containing more than 4,000 objects (thumbnails below, click to download full slide):

click to download full slide IP.307625

click to download full slide IP.307626

click to download full slide IP.307627

click to download full slide IP.307628

Each set of slide images was processed through segment, focus, and run2dmorph, for 2D morphometrics and on-going 3D morphometric research. The complete 2D dataset is available here: