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@MicroscopyImagingAnalysis

MicroscopyImagingAnalysis

README.md

Microscopy Imaging Analysis

This organisation was created to bring together and document the code used to process and analyse heterogeneous microscopy imaging data.

The repositories provide reusable methods with explicit pixel-based parameters and traceable data products from image intake to biological interpretation.

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microscopy-analysis-workflows is the visual, notebook-based entry point. Its ordered walkthrough covers image inspection, segmentation, 2D/3D measurements, spheroid radial analysis, spatial graphs, VAE/CVAE representations and analysis-ready feature tables.

Its four concise examples sit alongside the complete notebook walkthroughs.

Repositories

  1. microscopy-analysis-workflows: visual entry point, concise run modes and ordered notebooks
  2. nuclear-imaging-core: segmentation, measurements and spatial graph representations
  3. nuclear-spheroid-analysis: 2D/3D nucleus-to-spheroid and radial workflows
  4. nuclear-vae-embeddings: VAE and conditional VAE representations of nuclear crops
  5. nuclear-table-tools: feature-table joins, filtering and preparation

Each repository keeps scientific parameters visible in code or JSON config, separates reusable methods from workflow narrative, and uses stable object identifiers between processing stages.

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  1. microscopy-analysis-workflows microscopy-analysis-workflows Public

    Visual notebook workflows for quantitative microscopy image analysis

    Jupyter Notebook

  2. nuclear-imaging-core nuclear-imaging-core Public

    2D/3D microscopy segmentation, measurements and spatial graph representations

    Python

  3. nuclear-spheroid-analysis nuclear-spheroid-analysis Public

    Two- and three-dimensional nuclear spheroid analysis

    Python

  4. nuclear-table-tools nuclear-table-tools Public

    Filtering, joining and preparation of microscopy feature tables

    Python

  5. nuclear-vae-embeddings nuclear-vae-embeddings Public

    VAE and conditional VAE representations for nuclear microscopy crops

    Python

Repositories

Showing 6 of 6 repositories

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