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CyFi is a command line tool that uses satellite imagery and machine learning to estimate cyanobacteria levels in small, inland water bodies. The goal of CyFi is to help water quality managers better allocate resources for in situ sampling, and make more informed decisions around public health warnings for critical resources like lakes and reservoirs.

Read more atcyfi.drivendata.org

Install CyFi with pip:

pip install cyfi

Alternatively, CyFi can be installed with conda:

conda install -c conda-forge cyfi

For detailed instructions for those installing python for the first time, see theInstallation page.

Generate batch predictions at the command line withcyfi predict.

First, specify your sample points in a csv with the following columns:

• latitude
• longitude
• date

For example,

# sample_points.csvlatitude,longitude,date41.424144,-73.206937,2023-06-2236.045,-79.0919415,2023-07-0135.884524,-78.953997,2023-08-04

Then run:

cyfi predict sample_points.csv

This will output apreds.csv that contains a column for cyanobacteria density and a column for the associated severity level based on WHO thresholds.

# preds.csvsample_id,date,latitude,longitude,density_cells_per_ml,severity7ff4b4a56965d80f6aa501cc25aa1883,2023-06-22,41.424144,-73.206937,34173.0,moderate882b9804a3e28d8805f98432a1a9d9af,2023-07-01,36.045,-79.0919415,7701.0,low10468e709dcb6133d19a230419efbb24,2023-08-04,35.884524,-78.953997,4053.0,low

To see all of the available options, runcyfi predict --help.

Or, generate a cyanobacteria estimate for a single point on a single date usingcyfi predict-point.

Just specify the latitude, longitude, and date as arguments at the command line.

cyfi predict-point --lat 41.2 --lon -73.2 --date 2023-09-14

This will print out the estimated cyanobacteria density and associated severity level based on WHO thresholds.

2023-10-04 16:25:40.581 | SUCCESS  | cyfi.cli:predict_point:154 - Estimate generated:date                    2023-09-14latitude                      41.2longitude                    -73.2density_cells_per_ml        32,820severity                  moderate

To see all of the available options, runcyfi predict-point --help.

Severity levels are based on World Health Organization (WHO) cyanobacteria density thresholds.

• Low: 0 - 20,000 cells/ml
• Moderate: 20,000 - 100,000 cells/ml
• High: > 100,000 cells/ml

However users should feel free to to use their own thresholds as makes sense for their needs.

Launch theCyFi Explorer to view the Sentinel-2 imagery used to generate each cyanobacteria estimate!

Dorne, E., Wetstone, K., Cerquera, T. B., & Gupta, S. (2024). Cyanobacteria detection in small, inland water bodies with CyFi. In Proceedings of the 23nd Python in Science Conference (pp. 154–173).https://doi.org/10.25080/pdhk7238