Source portal: ZooScan Database (SIO Ocean Informatics / Mark Ohman Lab;
interface by Marina Frants) — https://oceaninformatics.ucsd.edu/zooscandb/
Acquired by: libs/download_zooscan.R (committed in CalCOFI/workflows),
2026-06-26, for issue CalCOFI/workflows#32.
Why this is scraped, not downloaded
The portal's "Download Data" button is disabled. The only data path is the
PRPOOS plot CGI /cgi-bin/tssubplot_new.py, which returns an interactive
Plotly page that embeds the underlying per-station values as a
data:text/csv;charset=utf-8,... download URI. download_zooscan.R authenticates
(public login), requests each bioclass in both plot modes with
pquant=Stations, and parses that embedded CSV.
Query parameters (held constant)
| param | value |
|---|---|
pquant |
Stations (per-station individual values, not means) |
linesel |
Both (CalCOFI lines 80 + 90; line 87 also present) |
daynight |
DayNight (both) |
plotlines |
SepLines |
showlims |
show |
mode |
basic → Abundance (No./m²) + Estimated C Biomass (mgC m⁻²); extra → Feret Diameter (mm) + Carbon Content (µgC individual⁻¹) |
bioclass |
one of 23 individual bioclasses (aggregate "Sum of all…" classes excluded) |
The basic and extra extracts per bioclass are joined on the shared station
key into zooscan_prpoos.csv. See _manifest.csv for per-class row counts.
Notes
- Coverage: CalCOFI lines 80/87/90, cruises 2005-present (PRPOOS / CCE-LTER
Process series). Cruise code =
YYYYMM+ 2-letter ship code. measurement_value = 0= the class was imaged but absent at that sample; every bioclass is reported at every station (dense per-class coverage).- Re-run reproducibly by deleting
zooscan_prpoos.csv(oroverwrite_all = TRUE) and re-renderingingest_cce-lter_zooscan.qmd.