napari-reco-plugin 0.1.6

A Napari plugin for tomographic reconstruction using the ASTRA Toolbox, with optional Paganin phase retrieval filter for phase-contrast data.

Reconstruction Napari Plugin

A Napari plugin for tomographic reconstruction using the ASTRA Toolbox, with optional Paganin phase retrieval filter for phase-contrast data.

Supported reconstruction algorithms: FBP, BP, SIRT, SART, CGLS — all available in CPU or GPU (CUDA) mode.

Installation

Option 1 — Install from Napari Hub (recommended)

Once published, the plugin can be installed directly from the Napari plugin manager:

1. Open Napari
2. Go to Plugins > Install/Uninstall Plugins
3. Search for "napari-reco-plugin"
4. Click Install

Alternatively, install via pip:

pip install napari-reco-plugin

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Option 2 — Manual installation (development)

1. Create and activate a conda environment

conda create -n napari-env python=3.12
conda activate napari-env

2. Install main dependencies

conda install -c conda-forge napari pyqt
conda install -c astra-toolbox -c nvidia astra-toolbox

# Ensure compatibility with ASTRA
pip install numpy==1.26.4

# Install CuPy depending on your CUDA version
pip install cupy-cuda12x  # or cupy-cuda11x

3. Clone the repository

git clone https://github.com/Clementcmoi/Reconstruction-napari-plugin.git
cd Reconstruction-napari-plugin

4. Install the plugin

pip install -e .

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Requirements

Core

• Python ≥ 3.9
• Napari
• ASTRA Toolbox

Optional (for GPU acceleration)

• CUDA Toolkit
• CuPy

⚠️ GPU dependencies are not installed automatically. You must install them manually according to your system configuration.

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Usage

Start Napari:

napari

Then open the plugin via:

Plugins > Reconstruction Plugin

Available tools:

• Reconstruction
• Multi Paganin

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Launchers Templates

Template scripts for launching Napari with the correct environment are available in the launchers/ folder.

Usage

1. Copy a .bat file from launchers/

2. Edit:

   • <path_to_conda> → your Anaconda/Miniconda path
   • <your_napari_env> → your environment name

3. Double-click to launch

Desktop shortcut (optional)

• Right-click .bat → Send to Desktop
• (Optional) Change icon via shortcut properties

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Project Structure

• Plugin source code: src/reco_plugin/
• Plugin manifest: src/reco_plugin/napari.yaml

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License

This project is licensed under the GNU General Public License v3.0 (GPL-3.0), in compliance with the ASTRA Toolbox license.