hypervolume is an R package that estimates n-dimensional hypervolumes from observed data. It can calculate shapes and volumes, perform set operations (intersection, union, etc.), detect holes, estimate probability density functions, project to geographic maps for species distribution modeling, and report functional diversity statistics. Supported geometries include kernel density estimation (hyperbox and Gaussian kernels), one-class support vector machine, and convex polytope (hulls). CRAN download. Github repository. Frequently asked questions.

LeafVeinCNN is a program co-developed with Mark Fricker and Hao Xu (Oxford) that automatically segments veins from images of leaf venation, then also extracts a spatial graph representation of the network, where edges correspond to individual vein segments of varying lengths and radii. These data are then used to calculate a range of single-scale and multi-scale statistics via hierarchical loop decomposition. The program uses deep learning algorithms (convolutional neural networks) trained on a wide range of input images to yield accurate results. Zenodo link.

thermal_analysis is a set of MATLAB programs that can radiometrically calibrate raw FLIR infrared image data based on external measurements of relative humidity, sky temperature, object distance, etc. The programs also allow for keypoint-based automatic registration of multiple frames and extraction of time series summary statistics. Github repository.

flir_thermal_control is a set of Python scripts and shell scripts for a Linux host (e.g. Raspberry Pi) that allow a FLIR camera to be controlled via a Gigabit ethernet interface. The code allows for automatic frame grabbing and recalibration at evenly spaced time intervals, for either linear temperature or for radiometric data. Github repository

leafarea estimates projected leaf area from scanned images of leaves. A variety of options are available to specify image resolution, reduce image noise, and fill holes in images. Images can be processed one at a time or in batches. Versions are available for ImageJ and for MATLAB (more feature-rich). Github repository.

comclim detects environmental mismatch and filtering in communities by integrating compositional data, climate niches, observed climate, and regional pools in a null modeling framework. CRAN download – Github repository

venation is a deprecated set of MATLAB programs that use traced skeletons of leaf venation networks to extract several summary statistics describing the geometry and topology of the network (e.g. vein density, loopiness, areole elongation index). Other programs allow rapid estimation of vascular bundle radius. The programs can work on user-defined regions of interest and variable resolutions in either a single image or batch processing mode. Github repository. Please use LeafVeinCNN (link above) instead as it is much more powerful!

timeordered is an R package that constructs time-ordered networks in which the links between nodes can change over time. It can also perform spreading analyses, project networks to time-aggregated networks, and report summary statistics over time. Website – CRAN download – Github repository

herbivory is a MATLAB program that allows delineation of leaf boundaries by a user to infer herbivory rates. Several damage types can also be scored. Github repository

Cavendish is a Mac OS X program that simulates gravitational interactions and collisions between many objects of variable sizes and masses. A 3-dimensional version and a 2-dimensional educational version are available. Full program. Education version of program.

Structure is a Mac OS X screensaver that visualizes protein geometry based on PDB files. Website