This respository is designed for analysis of aerial imagery of deciduous trees. It can be readily used with my imagery of Harvard Forest, available here, although some changes to file naming conventions and local directory paths will be needed. There is functionality to link with my preprocessed version of the Harvard Forest species map, which is available here in the 'metadata' directory. This code is oriented toward analysis of individual trees, although similar principles can be used to analyze images on a regularly spaced grid (i.e. 10 m). My published work based on this code is referenced below. Please cite the data sets or references accordingly if you use it.

This code was written with Matlab R2017a and makes use of the mapping toolbox (and possibly other toolboxes). Example output files for the mask drawing and image processing have been created for stem tag 311519.

• display_species_map: interactive plot of aerial image and tree stem locations, allowing identification of species and stem tag number
• species_color_guide: plot of legend with species color codes

May need to change image file name conventions, and path to images in these.

• create_masks: for spring time images
• create_masks_fall: fall

Auxiliary functions

• display_all_images
• display_images_fall

For redoing masks:

• redo_masks_spring
• redo_masks_fall

Time series data of color indices; see below references for context.

• create_tree_mask_time_series
• plot_tree_mask_time_series

Estimate curve fit parameters and phenology dates for individual trees.

• master_function

The rest of the functions are auxiliary for curve fit and date calculation. This workflow has been tested with the following configurations, which can be specified in master_function, to produce curve fits (i.e. running VI_curve) and get phenology dates (getPhenoDates):

To estimate spring and fall dates using GCC -

• index_type = 'gcc';
• model_name = 'greenDownSigmoid';
• date_method = 'CCR';

or using RCC -

• index_type = 'rcc';
• model_name = 'smoothInterp';
• date_method = 'spring_fall_red';
• percentiles = [0.1 0.5 0.9];

Note that the percentiles here refer to spring; in fall the date of maximum RCC is reported as the phenology date. These analysis functions show graphs of the curve fit and phenology dates and were designed to show 30 total trees; please adjust the subplot grid as necessary.

This is the most pertinent reference for this library of code, reporting on phenology analysis of individual trees:

• http://www.mdpi.com/1424-8220/17/12/2852

These references use phenology analysis of aerial imagery on a square grid:

• https://www.sciencedirect.com/science/article/pii/S0168192317303350
• https://link.springer.com/article/10.1007/s00484-018-1564-9