a package for analyzing spatial transcriptomic features of smFISH images
Project description
STProfiler
Spatial transcriptomics profiler (STProfiler) is a package dedicated for extracting subcellular spatial transcriptomics feautres from smFISH images.
Description
STProfiler includes image analysis, feature extraction and cell classification.
STProfiler is currently under development
Getting Started
Dependencies
STProfiler requires Python 3.8 orr newer. Addtional package dependencies include:
- numpy (>= 1.24.4)
- scipy (>= 1.10.1)
- matplotlib (>= 3.7.5)
- seaborn (>= 0.13.2)
- pandas (>= 2.0.3)
- scikit-learn (>= 1.3.2)
- scikit-image (>= 0.21.0)
- imbalanced-learn (>= 0.12.3)
- tqdm (>= 4.66.4)
- pillow (>= 10.3.0)
For cell segmentation purposes, Segment-Anything is required. Please refer to its github page for additional package dependencies.
Installing
Create a new conda environment
conda create -n stp_env python=3.8
conda activate stp_env
STProfiler is currently available on Test-PyPI
License
This project is licensed under the MIT License - see the LICENSE.md file for details
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