Systems Biology Practical Course 2026

Modules

1. Preprocessing
2. Cell Segmentation
3. Cell Phenotyping
4. Cell Neighbourhood Analysis

Repo Structure

sysbio2026/
├── Neighbourhood Analysis/
│ └──
├── phenotyping/
│ ├── README.md
│ ├── requirements.txt
│ └── src/
│ ├── 1_scimap_clustering.ipynb
│ ├── 2_scimap_prior.ipynb
│ ├── 3_compare_annotations.ipynb
│ └── 4_train_classifier.ipynb
├── pre-processing/
│ └──
└── segmentation/
└──