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emir-radkevich/README.md

About me

Computational Scientist at the Icahn School of Medicine at Mount Sinai, building Python pipelines for spatial and single-cell biology. I work across 10x Visium/Xenium, scRNA-seq, and high-plex imaging (Orion MxIF), designing tools like visium_analysis — used directly in a 2026 Science publication — and PathoLytica, an HPC-scaled imaging pipeline processing 1TB+ tissue image batches, used in a JCI 2025 paper. PathoLytica in my account is a public reference implementation; production version is institutional. Co-author on 9+ papers in Science, Nature, and Immunity.

Stack: Python (scanpy, lazyslide, SpatialData, scikit-learn), R (Seurat), Nextflow, Docker, LSF/Slurm.

Reach me:

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  1. PathoLytica PathoLytica Public

    End-to-end computational pipeline for multiplexed immunofluorescence processing

    Python 1

  2. ismms-himc/visium_analysis ismms-himc/visium_analysis Public

    Python package for neighborhood and gradient gene analysis in 10X Visium samples

    Python

  3. claude-skills claude-skills Public

    Claude skills for data analysis: visium-gradient-analysis. PathoLytica incoming

    Python

  4. ismms-himc/Bashore_aneurysm ismms-himc/Bashore_aneurysm Public

    Example code used in the aneurysm project, Bashore et al

    Jupyter Notebook

  5. scimap scimap Public

    Forked from labsyspharm/scimap

    Spatial Single-Cell Analysis Toolkit: closed PR (https://github.com/labsyspharm/scimap/pull/136)

    Python

  6. squidpy_notebooks squidpy_notebooks Public

    Forked from scverse/squidpy-tutorials

    Tutorials for Squidpy: pending PR (https://github.com/scverse/squidpy-tutorials/pull/144)

    Jupyter Notebook