seastartool 0.17

The Sea-faring System for Tagging, Attribution and Redistribution (SeaSTAR) is a GUI and CLI application for processing biodiversity data collected at sea.

SeaSTAR (Sea-faring System for Tagging, Attribution and Redistribution) is a CLI and GUI application for processing biodiversity data collected at sea.

Use cases

Currently SeaSTAR focuses on processing data collected on the IFCB instrument. It has functionality for interactions with EcoTaxa and CRAB.

How to install and basic use

$ pip install seastartool
Collecting seastartool
  Downloading seastartool-0.1-py3-none-any.whl.metadata (1.1 kB)
[...]
Successfully installed seastartool-0.1

SeaSTAR has in-built help which you can access using:

$ seastar --help

For more guides on how to use the software (such as to extract features or generate EcoTaxa tables), see the wiki.

An example with the IFCB

Given an example data:

raw/
  D20250810/
    D20250810T164958_IFCB225.adc
    D20250810T164958_IFCB225.hdr
    D20250810T164958_IFCB225.roi
    D20250810T171346_IFCB225.adc
    D20250810T171346_IFCB225.hdr
    D20250810T171346_IFCB225.roi
    D20250810T173732_IFCB225.adc

Extracting features (IFCB)

$ seastar ifcb_v4_features -i raw/D20250810/*.hdr -o features/D20250810/

Creating EcoTaxa tables

$ seastar ifcb_to_ecotaxa -i raw/D20250810/*.hdr ./metadata/A16N_metadata_filtered.csv --operator "Sample Operator" --qcdby "Sample Supervisor" --project "Sample Project" --nonull --ship "Sample Ship" --depth 5 -o