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Diving Deep
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Diving Deep
93 followers · 63 following

Achievements

Achievement: Pair Extraordinairex3Achievement: Pull Sharkx3Achievement: Galaxy BrainAchievement: QuickdrawAchievement: Starstruckx2Achievement: YOLOAchievement: Arctic Code Vault Contributor

Achievements

Achievement: Pair Extraordinairex3Achievement: Pull Sharkx3Achievement: Galaxy BrainAchievement: QuickdrawAchievement: Starstruckx2Achievement: YOLOAchievement: Arctic Code Vault Contributor

Highlights

  • Pro

Organizations

@rendeirolab @Marsilea-viz

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Mr-Milk/README.md

Hi, I'm Yimin (Milk) 👋

Applied Data Scientist at Graph Therapeutics. Previously a postdoc at Rendeiro Lab, CeMM, building open-source Python tools for computational pathology, spatial omics and scientific visualization.

Google Scholar LinkedIn Email Python Rust JavaScript

🛠 Projects

LazySlide    wsidata

LazySlide + wsidata
Whole-slide image analysis for digital pathology, scverse-native, with the data and IO layer underneath

LazySlide stars wsidata stars 		Marsilea    legendkit

Marsilea + legendkit
Composable visualizations (complex heatmaps, UpSet, OncoPrint…) and painless matplotlib legends

Marsilea stars legendkit stars
More
python-hmr Hot module reload for Python
sciink Fast Inkscape extensions for scientific figures, in Rust
Aquila Spatial single-cell database and analysis platform

Earlier: SpatialTis · SpatialEntropy

📄 Selected publications

  • LazySlide: accessible and interoperable whole-slide image analysis. Zheng Y, et al. Nature Methods (2026) · DOI
  • Histological aging signatures for monitoring tissue-specific aging and disease. Abila E, Buljan I, Zheng Y, et al. Nature Medicine (2026) · DOI
  • Marsilea: an intuitive generalized paradigm for composable visualizations. Zheng Y, et al. Genome Biology (2025) · DOI
  • Aquila: a spatial omics database and analysis platform. Zheng Y, et al. Nucleic Acids Research (2023) · DOI

→ Full list on Google Scholar

Pinned Loading

  1. Marsilea-viz/marsilea Marsilea-viz/marsilea Public

    Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)

    Python 327 15

  2. rendeirolab/LazySlide rendeirolab/LazySlide Public

    Accessible and interoperable whole slide image analysis for digital pathology in Python

    Python 334 32

  3. Marsilea-viz/legendkit Marsilea-viz/legendkit Public

    Legend made easy for matplotlib

    Python 36

  4. rendeirolab/wsidata rendeirolab/wsidata Public

    Efficient data structures and IO for whole slide image analysis

    Python 34 6

  5. SpatialTis SpatialTis Public archive

    Spatial analysis toolkit for single cell multiplexed tissue data

    Python 30 1

  6. python-hmr python-hmr Public

    🔄 Hot module reload for python, automatically reload your code when files are modified. No need to modify source code.

    Python 34 1