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aquab1t/README.md

Hi, I'm José Manuel

Oceanographer & Geospatial Scientist | Former Automation Engineer

I bridge the gap between systems engineering and marine science. As an automation engineer turned PhD Candidate in Marine Sciences, I build end-to-end data pipelines for satellite remote sensing and develop ocean hydrodynamic models to study ecological connectivity.

What I'm Working On

  • Kelp Forest Dynamics: Detecting Nereocystis luetkeana and Macrocystis pyrifera from Sentinel-2 imagery across the Northeast Pacific (2015–2025).
  • Kelp Spore Dispersal Modeling: Simulating population connectivity in British Columbia using the FVCOM hydrodynamic model (804K-node unstructured mesh) paired with OpenDrift/OceanParcels Lagrangian particle tracking.
  • Sargassum Detection: Classifying pelagic Sargassum in the Caribbean Sea and Equatorial Atlantic using machine learning pipelines on Aqua-MODIS, Sentinel-3 OLCI, Sentinel-2 MSI, and Landsat-8/9 OLI data.

Tech Stack & Tools

Languages & Environments

Python R C++ Jupyter Linux

Machine Learning & Data Science

TensorFlow PyTorch Keras Scikit-Learn Pandas NumPy

Geospatial & Earth Observation

QGIS Google Earth Engine

  • Earth Observation: MODIS-Aqua, Sentinel-2 MSI, Sentinel-3 OLCI, Landsat-8/9 OLI, Ocean Color, Spectral Indices
  • Machine Learning: XGBoost, Random Forest, KNN, 1D/2D-CNN, MLP
  • Ocean Modeling: FVCOM, OpenDrift, OceanParcels, HYCOM, CMEMS, GLORYS12, ERA5, TPXO10, pyTMD
  • Geospatial Processing: GRASS, GDAL/OGR, GeoPandas, Cartopy, Rasterio, OpenDroneMap

Background

  • PhD in Marine Sciences - CICIMAR-IPN, Mexico (Expected Jul 2026)
  • Fellowship - NF-POGO Centre of Excellence, Dalhousie University, Canada (2024–2025)
  • MSc in Marine Resources Management - CICIMAR-IPN, Mexico (2022)
  • BSc in Automation Engineering - CUJAE, Cuba (2015)

Let's Connect

LinkedIn ORCID Email

Pinned Loading

  1. seabed-mapping-project seabed-mapping-project Public

    Course project report and code for Geostatistics and Seabed Characterization

    Python 1 1

  2. 3d_ocean_geobody 3d_ocean_geobody Public

    This repository contains the supplementary material for the study presented at the 12th Ocean of Data Challenge. The project demonstrates a machine learning workflow to transform sparse underwater …

    HTML

  3. kelp-detection-sentinel2 kelp-detection-sentinel2 Public

    Kelp forest detection from Sentinel-2 imagery using a 2D-CNN (SepConv-SE, 4 classes, 93.7% test accuracy). Pre-trained TFLite models + 148-scene Cedros Island case study (2015–2025) analysing cloud…

    Python

  4. odm-dji odm-dji Public

    Interactive ODM launcher for DJI drones, auto-detects camera model and injects lens calibration

    Python

  5. sargassum-satellite-ml sargassum-satellite-ml Public

    ML pipeline for detecting pelagic Sargassum from Sentinel-2/MODIS/Landsat-8 satellite imagery. Models: XGBoost, 1D-CNN, MLP. Outputs fractional cover maps at 10m resolution. Website: https://doi.or…

    Python 1