Metadata-Version: 2.4
Name: dicella
Version: 0.0.10
Summary: Digital Cell Analysis Toolkit
Author-email: Hailin Pan <hailinpan1988@163.com>
License: MIT
Project-URL: Homepage, https://github.com/HailinPan/dicella
Project-URL: Repository, https://github.com/HailinPan/dicella
Keywords: cell-analysis,bioinformatics
Classifier: Development Status :: 1 - Planning
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.9
Description-Content-Type: text/markdown
Requires-Dist: numpy>=1.24
Requires-Dist: pandas>=2.0
Requires-Dist: scipy>=1.10
Requires-Dist: opencv-python>=4.8
Requires-Dist: scikit-image>=0.21
Requires-Dist: scikit-learn>=1.3
Requires-Dist: anndata>=0.9
Requires-Dist: matplotlib>=3.7
Requires-Dist: seaborn>=0.12
Requires-Dist: plotly>=5.0
Provides-Extra: seg
Requires-Dist: cellpose>=3.0; extra == "seg"
Provides-Extra: all
Requires-Dist: cellpose>=3.0; extra == "all"

# DiCellA

**Digital Cell Analysis Toolkit**

This package is a digital cell analysis toolkit that provides a set of tools for cell analysis.

## Repository
- [DiCellA in GitHub](https://github.com/HailinPan/dicella)

## Installation

### Core installation (without cell segmentation)
```bash
# create a new conda environment
conda create -n dicella_env python=3.11 -y
conda activate dicella_env

# install from PyPI (core only, no cellpose/GPU required)
pip install dicella

# or install from GitHub
pip install git+https://github.com/HailinPan/dicella.git
```

### Full installation (with cell segmentation)
Cell segmentation depends on [Cellpose](https://github.com/MouseLand/cellpose), which requires PyTorch and a CUDA-enabled GPU.
```bash
# option 1: install dicella with the [seg] extra
pip install "dicella[seg]"

# option 2: install cellpose separately, then dicella
pip install cellpose
pip install dicella

# option 3: install everything at once from GitHub
pip install "git+https://github.com/HailinPan/dicella.git#egg=dicella[seg]"
```

### Verify installation

```bash
# check core import works (no cellpose needed)
python -c "import dicella; print(dicella.__version__)"

# check CLI is available
dicella --help

# if you installed with [seg], check cell segmentation import
python -c "from dicella.cell_seg import cell_seg_on_ssdna_by_cellpose; print('cellpose OK')"
```

