Satellite Chlorophyll Data Visualization

Option 1:
Load a file with predefined settings (.csv, created in PhytoFit): Browse to select, then click "Apply settings".


Option 2:
Start selecting your settings below, then click "Load data" and adjust remaining settings as needed.


Satellite / spatial resolution
**1km-resolution data only exists in a box encompassing the Gulf of Saint Lawrence (41-53 N, 49-75 W), using the EOF algorithm Region
Chlorophyll algorithm
**EOF data only exists in a box encompassing the Gulf of Saint Lawrence (41-53 N, 49-75 W) View full satellite [chla], or use one of two models to separate satellite [chla] into concentrations of different phytoplankton cell sizes, and choose the cell size to view:

Year
Data composite length
Log chlorophyll

Adjust map colour scale
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Choose day of year
Enter the day of year and click "Go", or drag the slider to view the map for that day. Use the "play/pause" button on the slider to move through a sequence of daily/weekly chlorophyll maps automatically.
NOTE: If you are viewing weekly (8-day) data, the day of year will reset to the first day of the selected week.

(Optional) Enter a name (use only alphanumeric characters, underscores, or periods) and click "Apply".
Choose the method to create your polygon.
Draw polygon using the toolbar at the top left corner of the map.
Enter decimal latitudes and longitudes for vertices of polygon, separated by commas, then click "Create polygon". Use lon/lat < 0 for west/south. Lists must be the same length, with >2 values each, in the same order so that each latitude is paired with longitude.
Click "Browse" to find a shapefile. Select the "shp" file and all files with the same name but different extensions (e.g. dbf, prj, sbx...), then "Open". If the polygon does not load automatically, click "Create polygon" (NOTE: polygons with a large number of vertices may take several seconds to load). Warning: This will only use the first polygon in the shapefile, and disjoint polygons are NOT allowed.
List of latitudes:
List of longitudes:



Minimum daily/weekly % coverage
Days with less than the minimum percent coverage in the selected polygon will not be plotted on the density plot or time series, or used in the bloom fit.
Outlier detection method
SD = standard deviation
IQR = interquartile range
Daily/weekly statistic
Choose to use either daily/weekly mean or median chlorophyll in the time series and bloom fit.
Range of pixel values
Choose the range of values allowed in the calculation of the statistics and bloom fit (pixels outside this range will be omitted).
If a limit is left blank, it will be ignored.
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Choose fit method, bloom shape, and point smoothing method.
LOESS span
Controls the degree of smoothing.
Set the range of days to use in the bloom fit, and the limits of the day of maximum concentration and the first day of the bloom.
Select the method used to calculate tstart :
Either 20% of the curve amplitude (peak minus background), or a constant threshold between 0.05 and 1 (difference between the fitted curve and background chla, calculated in linear space).
Switch to ON to consider tmax a parameter in the regression.
WARNING: This will disable tstart limits.
Switch to ON to allow background chlorophyll B0 to vary as a function of day.
Switch to ON to weight each daily/weekly point in the fit by percent coverage.
When calculating magnitude (area under the curve between tstart and tend) and amplitude of the bloom, should the background be removed first?
Flags
Fits will be flagged if they meet certain criteria that indicate potential problems with the fit (NOTE: this does not affect the fit itself). Combinations of flags will be written as a single number (for example, 13 for flags 1 and 3). Click below for details. Optionally adjust the parameters of some flags.


Flag 1: Amplitude ratio limits
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Flag 2: Magnitude ratio limits
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Threshold coefficient
The start of the bloom is considered to be the point before tmax when chlorophyll concentration drops below a threshold for > 14 days.
Threshold = chlamed * threshold coefficient
chlamed = UNLOGGED median chlorophyll
NOTE: If log10chla is ON, the resulting theshold will be logged.



Save settings (.csv)
Time series
Select a series of years and the polygons you would like to process using the current settings, then click "Run time series" to generate the following:
Files will be zipped to a folder following the naming convention satellite_ region_ compositeLength_ years_ cellSizes_ chlaAlgorithm_ fitmethod_ timecreated.
Make sure at least one polygon is selected.
When processing is complete and the new filename appears over the download button, click "Download results (.zip)".

Download results (.zip)
Download map (.html)


Download density plot (.png)

Download time series plot of daily/weekly chlorophyll (.png) Download time series table of statistics (.csv) Download fitted bloom parameters (.csv)