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Datasets

Data source and Modalities in Recent Aquaculture/Ocean Literature

• Surface Water Quality
  Task: Monitoring; Modality: Tabular; Feature: Global surface water quality measurements
  Primary Article/Citation: Karim et al. (2025)
  Open Access: Link

• World Ocean Database
  Task: Monitoring; Modality: Tabular; Feature: Large-scale oceanographic observations
  Primary Article/Citation: Mishonov et al. (2025)
  Open Access: https://www.ncei.noaa.gov/products/world-ocean-database

• Water Quality Metrics of Pond
  Task: Monitoring; Modality: Tabular; Feature: Sensor-based pond water monitoring
  Primary Article/Citation: Islam et al. (2023)
  Open Access: https://www.sciencedirect.com/science/article/abs/pii/S0141933123001746

• DeepFish
  Task: Segmentation; Modality: RGB; Feature: Fish instance segmentation dataset
  Primary Article/Citation: Nahuel et al. (2022)
  Open Access: https://github.com/icclabo/DeepFishDatasetScripts

• Fish4Knowledge
  Task: Tracking; Modality: Multi-camera; Feature: Large-scale reef fish video dataset
  Primary Article/Citation: Fisher et al. (2016)
  Open Access: https://github.com/icclabo/Fish-Detection-Tracking-and-Classification

• FishNet
  Task: Recognition; Modality: RGB; Feature: Fish species recognition benchmark
  Primary Article/Citation: Khan et al. (2023)
  Open Access: https://github.com/icclabo/FishNet

• FishTrack23
  Task: Segmentation; Modality: RGB; Feature: Underwater image segmentation benchmark
  Primary Article/Citation: Dawkins et al. (2023)
  Open Access: https://github.com/icclabo/ConvertFishTrack23

• DIDIDSONAR
  Task: Identification; Modality: Sonar; Feature: DIDSON sonar fish identification dataset
  Primary Article/Citation: McCann et al. (2018)
  Open Access: Link

• SOLAQUA
  Task: Autonomous; Modality: Multimodal; Feature: Autonomous aquaculture perception dataset
  Primary Article/Citation: Ohrem et al. (2025)
  Open Access: https://data.sintef.no/feature/fe-a8f86232-5107-495e-a3dd-a86460eebef6

• AQUALOC
  Task: Autonomous; Modality: Multimodal; Feature: Multimodal underwater localization dataset
  Primary Article/Citation: Ferrera et al. (2019)
  Open Access: https://www.lirmm.fr/aqualoc/

• FCNet
  Task: Counting; Modality: RGB; Feature: Multi-scale fish counting dataset
  Primary Article/Citation: Wang et al. (2025)
  Open Access: https://github.com/icclabo/FCNet

Software

Convex Tools and Solvers:

• CVX - A MATLAB-based modeling system used for defining and solving disciplined convex programs (DCPs).
• SeDuMi - A Matlab/GNU Octave package for solving convex optimization problems involving linear equations and inequalities, second-order cone constraints, and semidefinite constraints (linear matrix inequalities).
• SDPT3 - A MATLAB software for semidefinite-quadratic-linear programming.
• Gurobi - A commercial mathematical optimization solver (engine) used for decision intelligence and prescriptive analytics.
• MOSEK - A specialized, high-performance software package designed for solving large-scale mathematical optimization problems.
• GLPK - A GNU Linear Programming Kit is a software package intended for solving large-scale linear programming, mixed integer programming, and other related problems.

Statistics Software:

• wcc - An experimental R package for conducting windowed cross-correlation analyses.
• varde - An experimental R package for decomposing the variance in mixed effects models.
• agreement - An experimental R package for estimating inter-rater reliability.

Quarto Extensions

• lordicon - A stable Quarto extension for embedding animated Lordicon icons in HTML.
• honeypot - An experimental Quarto extension for detecting LLM cheating on HTML assignments.
• details - A stable Quarto extension for embedding interactive details blocks in HTML documents.
• embedpdf - A stable (but questioning) Quarto extension for embedding PDF files in HTML.

Docker Images:

• rstudio2u - A multiarchitecture (amd64/arm64) image combining rstudio and r2u
• rocker-bayes - A multiarchitecture (amd64/arm64) image for Bayesian analysis in R
• wsl-whisper - A WSL (amd64) image for AI transcription from R with CUDA-support