プロフィール詳細

プロジェクトを作成

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Dr. SiTong H.に依頼

Canada

Vascular biology PhD candidate — custom Python pipelines for microscopy quantification & single-cell analysis

プロフィール概要

I'm a PhD candidate in Biomedical Engineering at the University of Toronto (vascular biology), and I build image analysis and single-cell pipelines. My thesis work required quantifying microvessel networks from confocal data. AngioTool misreads hollow-lumen structures and default ImageJ macros count isolated cells as vessel segments, so I built my own pipeline in Python: lumen detection, isolated-object filtering, skeletonization metrics for length, branch points and network density. I handle Leica .lif Nikon.nis and Zeiss.czi and other proprietary formats, including batch processing. I also run snRNA-seq analysis end to end — Seurat clustering, cell type annotation, CellChat ligand–receptor inference — plus bulk RNA-seq (Salmon, DESeq2). I do the wet lab work too: hPSC-derived endothelial cells, macrophages and fibroblasts, co-culture and chemotaxis assays, in vivo models, confocal imaging. That's the part that matters for analysis — I know what the assay was measuring and where the artifacts come from. Deliverables include the pipeline, documented outputs, and methods text you can adapt for a manuscript. Tools: Python (scikit-image, NumPy, pandas, OpenCV), R (Seurat, CellChat, DESeq2), ImageJ/Fiji macros, Git

専門分野

• ☆ Biochemistry
• ☆ Immunoassay
• ☆ Molecular Biology
• ☆ Microarrays
• ☆ ATAC-Seq
• ☆ Gene Expression Analysis
• ☆ RNA Sequencing
• ☆ Microscopy
• ☆ Cryosectioning
• ☆ Light Microscopy
• ☆ Fluorescence Microscopy
• ☆ Python
• ☆ R

サービス

• Consulting
• Data & AI

Consulting Scientific and Technical Consulting

Data & AI Statistical Analysis, Image Analysis

職務経験

Researcher

Toronto general hospital

9月 2023 - 現在

University of Toronto

9月 2023 - 現在

学歴

PhD

University of Toronto

9月 2023 - 現在

PhD

University Health Network

9月 2023 - 現在

(Medicine)

Tsinghua University

9月 2020 - 6月 2023

University of Toronto

9月 2014 - 5月 2018

認定資格

• 認定資格の詳細は未入力です。

出版物

JOURNAL ARTICLE

Mengda Li, Peiliang Wang, Si Tong Huo, Hui Qiu, Chendi Li, Siyong Lin, Libin Guo, Yicong Ji, Yonglin Zhu, Jinyang Liu, et al. (2024). Human Pluripotent Stem Cells Derived Endothelial Cells Repair Choroidal Ischemia . Advanced Science.

Sitong Huo, Jing Yuan, Fei Lin, Zhiyong Wu, Zhilin Jiang, Ting Wang, Weinan Lai, Li Li, Chao Zhang (2023). Circ-CPSF1 Worsens Radiation-Induced Oxidative Stress Injury in Caenorhabditis elegans . Biomolecules.

Sitong Huo, Jing Yuan, Fei Lin, Zhiyong Wu, Zhilin Jiang, Ting Wang, Weinan Lai, Li Li, Chao Zhang (2023). Circ-CPSF1 Worsens Radiation-Induced Oxidative Stress Injury in <i>Caenorhabditis elegans</i> . Biomolecules.

Gao Y, Gao J, Lin F, Wang T, Huo S, Wu J, Zhou Q, Zhang C (2022). CircRNAs in Tumor Radioresistance . Biomolecules.

SI TONG HUO (2021). Circular RNA in tumor metastasis . Molecular therapy. Nucleic acids.

SI TONG HUO (2020). Rapid Development of Targeting circRNAs in Cardiovascular Diseases . Molecular therapy. Nucleic acids.