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ofen1996/README.md

Ouyang — Scientific Imaging & Computer Vision Engineer

Remote · Upwork Freelancer · Scientific Imaging Engineer
Python · OpenCV · PyTorch · Large-Scale Image Processing

What I Build

I design and ship production-grade image processing pipelines for scientific microscopy — from raw microscope tiles to quantifiable results.

Clients come to me when they have large imaging datasets (gigabytes to terabytes per experiment) and need:

Problem What I Deliver
Stitch 10,000+ FOV tiles into one seamless whole-slide image Memory-efficient pyramidal TIFF + libvips pipeline
Automatically find, count, and segment cells in microscopy images YOLO / U-Net / Watershed with ONNX inference
Decode fluorescence barcodes across 1020 hybridization cycles Multi-channel registration + Cy3/Cy5 ratio classification
Align multi-camera arrays with sub-pixel accuracy Chessboard calibration + homography estimation
Run heavy image jobs on HPC clusters SGE/Slurm schedulers, multiprocessing, error recovery

Portfolio — Selected Projects

Spatial Transcriptomics Barcode Decoder (S5000)

BioChip huge-chip pipeline — 117,800 barcodes per cycle, 18 cycles
Repo BMK_huge_decode_program_S5000
Stack Python, OpenCV, YOLOv5 (ONNX), libvips, OpenSlide, NumPy, SciPy
What it does FOV stitching, chip ROI search, barcode center detection, geometric correction, Cy3/Cy5 signal decoding, HPC-cluster orchestration
Result Fully automated decoding for 380x310 arrays; handles 40 GB+ whole-slide images

Light Field Imaging — Multi-Camera Array Calibration & Refocusing

3x3 camera array system with interactive shift-and-sum refocusing
Repo Light-field
Stack MATLAB, OpenCV, ORB Features, RANSAC Homography, GUI
What it does Chessboard calibration across 9 cameras, perspective rectification, shift-and-sum refocus, interactive MATLAB GUI
Result Real-time focal-plane adjustment from a single 9-camera exposure

Cell Segmentation & Spatial Barcode Mapping

  • Biomarker-cell_seg — Whole-slide cell boundary extraction, ROI analysis, spatial barcode-to-cell mapping
  • Python, OpenCV, ONNX Runtime, libvips, scikit-image

Large-Scale Whole-Slide Image Stitching

  • BMK-Huge-img-program — Register tiled FOVs, pyramidal TIFF composition, O(N log N) for 10K+ tiles
  • Biomarker-BMChiper-no-div — Whole-slide alignment, array localization, stitching
  • Python, OpenCV, ORB/SIFT, RANSAC Homography, libvips

Multi-Cycle Fluorescence Image Decoding

  • Decode_20X — Cross-cycle FOV registration + Cy3/Cy5 ratio-based base classification
  • Python, OpenCV, libvips, NumPy

Fourier Transform & Frequency-Domain Processing

  • ZTE2020Fourier-Preliminary — FFT experiments, spectrum analysis, frequency-domain filtering
  • Python, NumPy FFT, Matplotlib

Tech Stack

Python ecosystem
  NumPy, SciPy, Pandas — numerical / signal / data
  OpenCV, scikit-image, tifffile — computer vision & imaging
  PyTorch, scikit-learn, ONNX Runtime — ML & inference
  libvips, OpenSlide, h5py — large-image I/O

Infrastructure
  Linux, Bash, Docker, Git
  SGE / Slurm — HPC job schedulers
  CUDA — GPU acceleration (PyTorch, OpenCV dnn)

Image formats: TIFF, BigTIFF, OME-TIFF, MRXS (OpenSlide), HDF5

Services I Offer

  • Whole-slide / large-image stitching and registration
  • Cell segmentation and microscopy image analysis
  • Fluorescence / spatial transcriptomics decoding pipelines
  • Camera calibration and geometric transformation
  • Custom computer vision for scientific instruments
  • HPC cluster pipelines (SGE, Slurm, multiprocessing)
  • One-off script to production pipeline conversion

Let's Build Something
GitHub github.com/ofen1996
Email 526083628@qq.com
Location Remote

Open to Upwork contracts and technical collaborations. Reply to this repo or drop an email — I typically respond within 24 hours.

Pinned Loading

  1. Biomarker-BMChiper-no-div Biomarker-BMChiper-no-div Public

    Whole-slide image alignment, array localisation, and large-image stitching with Python, OpenCV, ONNX, and libvips.

    Python 1

  2. Biomarker-cell_seg Biomarker-cell_seg Public

    Cell segmentation, boundary extraction, and spatial barcode mapping for large microscopy images.

    Python 1

  3. Light-field Light-field Public

    End-to-end light field imaging pipeline: multi-camera (3x3) calibration via chessboard homography, perspective rectification preprocessing, and MATLAB GUI for interactive shift-and-sum refocusing.

    MATLAB 1

  4. BMK-Huge-img-program BMK-Huge-img-program Public

    Large-scale image alignment and multi-channel stitching using Python, OpenCV, ONNX, and libvips.

    Python

  5. BMK_huge_decode_program_S5000 BMK_huge_decode_program_S5000 Public

    大芯片解码

    Python

  6. Decode_20X Decode_20X Public

    Multi-cycle fluorescence image decoding, registration, and signal classification for large tiled images.

    Python