Pure Python Computed Tomography reconstruction web application. Built with Solara.

If you use alrecon please cite:

Iori et al., (2024). Alrecon: computed tomography reconstruction web application based on Solara. Open Research Europe, 4(54). https://doi.org/10.12688/openreseurope.16863.1

1. Checkout this repository:

git clone https://github.com/gianthk/alrecon.git

2. Navigate to the repository and create a virtual environment with all necessary dependencies:

cd alrecon
conda env create --file envs/alrecon-base.yml
conda activate alrecon-base

3. Build the alrecon app:

pip install -e .

solara run alrecon.pages --host localhost

1. Make sure that the alrecon virtual environment is activated and ipykernel installed:

conda activate alrecon
pip install --user ipykernel

or:

conda install -c anaconda ipykernel 

2. Install ipykernel with the alrecon virtual environment:

python -m ipykernel install --user --name=alrecon

3. Launch Jupyter Notebook or Jupyter Lab instance:

jupyter lab

4. Open and run the cells of the notebook launch_within_jupyter.ipynb.

You can take a look at solara's documnetation for more information on the different ways of running solara applications.

• Alrecon allows you to keep a consistent log of all reconstruction jobs on an online master Google spreadsheet.
• The integration uses gspread, a Python API for Google Sheets.
• You will need to setup your Google Cloud account, enable Google Sheets API, and create a Secret Key with read/write permission to your online master Google sheet. Follow these instructions to setup the integration with Google Sheets API.

napari is a powerful pure Python multi-dimensional image viewer. Alrecon supports napari only when running the app through Jupyter.

To launch ImageJ from the alrecon web app follow these steps:

1. Modify the path to your ImageJ executable in the alrecon general settings

2. Copy the FolderOpener_virtual.ijm ImageJ macro contained in /alrecon/imagej_macros/ to the plugin folder of your ImageJ installation. On Linux this is something like /opt/Fiji.app/macros/.

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No [822535](Beamline for Tomography at SESAME BEATS).