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Biofilm Percent Cover Maps in San Francisco Bay, 2020-2022

August 1, 2023

This data release includes 9 GeoTIFF rasters that represent percent cover of intertidal microbial biofilm on the mudflats of South San Francisco Bay, CA between June 2020, and June 2022. Rasters follow the naming scheme biofilmPC_YYYYMMDD_10m.tif, where “biofilmPC” describes the dataset, YYYYMMDD is the date of the image, and 10m is the spatial resolution of the raster. Raster data products were derived from 10m Sentinel-2 Muti-Spectral Imager (MSI) imagery, collected and maintained by the European Space Agency (ESA) and published for public access on Copernicus Data Hub ( The area of interest includes the Eden Landing Ecological Reserve and all tidally exposed mudflats within the bounds of San Francisco Bay proper, south of Hayward, CA. Maps report the percent cover of biofilm ranging from 0 to 1 and were generated via a series of processing steps in Python and VIPER tools in ENVI. The no data value is 0, reporting anywhere where there is no biofilm as a 0 value. The study area was constrained using a vector mask, then water and vegetated areas were recognized and removed using a series of indices, leaving only the mudflat areas. Data was imported to ENVI and run through Multiple Endmember Spectral Mixture Analysis (MESMA) in VIPER tools using a percent cover endmember library generated from an in-situ dataset. The accuracy of the raster data products was evaluated by comparing raster values to 43 reference data points taken around South San Francisco Bay, using linear regression. The R squared of the regression between raster percent cover values and in situ reference data was 53%. Accuracy was influenced by differences in scale between image data and in-situ reference data and possible error in image georectification.

Publication Year 2023
Title Biofilm Percent Cover Maps in San Francisco Bay, 2020-2022
DOI 10.5066/P9JHG4E1
Authors Nicole C Taylor, Kristin B Byrd, Sherry L Palacios, Isa Woo, Stacy M Moskal, Susan E De La Cruz
Product Type Data Release
Record Source USGS Digital Object Identifier Catalog
USGS Organization Western Geographic Science Center - Main Office