Installation

This guide will help you install the Napari Chromosome Analysis toolkit.

Requirements

The following are required to run this software:

Python 3.8 or higher
CUDA-compatible GPU (recommended for Cellpose)
At least 8GB of RAM

Dependencies

The main dependencies include:

napari - Multi-dimensional image viewer
cellpose - Cell segmentation
scikit-image - Image processing
numpy - Numerical computing
pandas - Data analysis
matplotlib - Plotting
magicgui - GUI widgets
qtpy - Qt abstraction layer

Installation Steps

Clone the repository:

git clone <repository-url>
cd napari_ui

Create a conda environment:

conda create -n napari-chr python=3.9
conda activate napari-chr

Install dependencies:

pip install napari cellpose scikit-image numpy pandas matplotlib magicgui qtpy superqt pillow

Install Cellpose model:

# The code expects a trained Cellpose model at:
# /gpfs/gsfs10/users/sagarm2/cellpose_chr/newDataSet/trainingfiles/models/cellpose_1718127286.8010929
# You may need to update the path in the code to point to your model

Test the installation:
```
python main.py
```

GPU Support

For optimal performance with Cellpose segmentation, ensure you have:

CUDA toolkit installed
Compatible GPU drivers
PyTorch with CUDA support

To install PyTorch with CUDA support:

pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu118

Troubleshooting

ImportError: No module named ‘napari’

Make sure you have activated the correct conda environment and installed all dependencies.

CUDA out of memory

Reduce the image size or use CPU-only mode by setting gpu=False in the Cellpose model initialization.

Qt application issues

Ensure you have a compatible Qt backend installed. Try:

pip install PyQt5

or:

pip install PySide2