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Hire Dr. SiTong H.

Canada

USD 60 /hr

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

Profile Summary

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

Subject Matter Expertise

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

Services

• Consulting
• Data & AI

Consulting Scientific and Technical Consulting

Data & AI Statistical Analysis, Image Analysis

Work Experience

Researcher

Toronto general hospital

September 2023 - Present

University of Toronto

September 2023 - Present

Education

PhD

University of Toronto

September 2023 - Present

PhD

University Health Network

September 2023 - Present

(Medicine)

Tsinghua University

September 2020 - June 2023

University of Toronto

September 2014 - May 2018

Certifications

• Certification details not provided.

Publications

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.