Paradinium-Oithona annotated images and count data

Human annotated images, machine learning derived count data, and environmental data associated with our paper " Discovery and dynamics of a cryptic marine copepod-parasite interaction" published in Marine Ecology Progress Series. The work is based on imagery generated by the Scripps Plankton Camera System deployed at the Scripps Pier in La Jolla, California, USA.

This repository contains:

human_annotated_SPC_data.zip - Regions of Interested collected by the SPC sorted by a human expert into relevant classes: Oithona, Oithona with parasite, and Oithona with eggs. Access to the "other" class is available upon request.

corrected_counts_091817.txt - Count data from the summer of 2015 generated a fine tuned deep neural network with associated human corrected counts.

oith_parasite_081420.txt - Count data from March 2015 - April 2016. Data collected after August 2015 is machine generated and should considered a maximum estimate of relative abundance.

autoss_a8bc_287c_07d6.csv - Environmental data measured by the automated shore station deployed at Scripps Pier and maintained the Southern California Coastal Ocean Observing System. Complete shore station data can be accessed via NOAA ERDDAP.