Microscopy TIFF stacks → Squid acquisitions

Install

Clone the Repository:

git clone https://github.com/maragall/flatfield_tool.git
cd flatfield_tool

Create & Activate Conda Environment:

conda create -n flatfield python=3.10 -y
conda activate flatfield

Install Dependencies with uv:

You can install it using pip:

pip install uv

Then, install the project dependencies:

uv pip install -r pyproject.toml

pip install basicpy

GUI

python -m flatfield.gui.flatfield_gui

CLI

flatfield compute /path/to/acq
flatfield apply  /path/to/flatfields_*  /path/to/acq1 …

Desktop Shortcut Setup (Ubuntu/Windows)

python3 create_desktop_shortcut.py