PyFigures will assist you assemble publication ready scientific figures in no time.
Project description
PyFigures
Effortless creation of high-quality scientific figures in Python.
Since a video is better than a thousand (click on the image above to view the demo).
Install
-
Install Miniconda (if not already present on your system)
-
Then in a command prompt type:
conda create -y -n PyFigures python==3.10.12
conda activate PyFigures
pip install -U pip
pip install -U pyfigures
python -m pyfigures
NB:
- To open a command prompt on Windows press Windows+R then type cmd
- To open a command prompt on MacOS press Command+Space then type Terminal
- To open a command prompt on Ubuntu press Ctrl+Alt+T
Run
To open the graphical user interface, type the following in a command:
conda activate PyFigures
python -m pyfigures
Third party libraries
Below is a list of the 3rd party libraries used by PyFigures.
IMPORTANTLY: if you disagree with any license below, please uninstall PyFigures.
Library name | Use | Link | License |
---|---|---|---|
Markdown | Python implementation of Markdown | https://pypi.org/project/Markdown/ | BSD |
matplotlib | Plots images and graphs | https://pypi.org/project/matplotlib/ | PSF |
numpy | Array/Image computing | https://pypi.org/project/numpy/ | BSD |
Pillow | Reads 'basic' images (.bmp, .png, .pnm, ...) | https://pypi.org/project/Pillow/ | HPND |
PyQt6 | Graphical user interface (GUI) | https://pypi.org/project/PyQt6/ | GPL v3 |
QtPy | An abstraction layer for PyQt and PySide | https://pypi.org/project/QtPy/ | MIT |
read-lif | Reads Leica .lif files | https://pypi.org/project/read-lif/ | GPL v3 |
czifile | Reads Zeiss .czi files | https://pypi.org/project/czifile/ | BSD (BSD-3-Clause) |
tifffile | Reads .tiff files (also reads Zeiss .lsm files) | https://pypi.org/project/tifffile/ | BSD |
python-bioformats | A library to open scientific images | https://pypi.org/project/python-bioformats/ | GPLv2 |
python-javabridge | A library to run java executables (required for bioformats) | https://pypi.org/project/python-javabridge/ | BSD |
scikit-image | Image processing | https://pypi.org/project/scikit-image/ | BSD (Modified BSD) |
scipy | Great library to work with numpy arrays | https://pypi.org/project/scipy/ | BSD |
scikit-learn | Great library for machine learning | https://pypi.org/project/scikit-learn/ | BSD |
tqdm | Command line progress | https://pypi.org/project/tqdm/ | MIT, MPL 2.0 |
natsort | 'Human' like sorting of strings | https://pypi.org/project/natsort/ | MIT |
numexpr | Speeds up image math | https://pypi.org/project/numexpr/ | MIT |
urllib3 | Model architecture and trained models download | https://pypi.org/project/urllib3/ | MIT |
qtawesome | Elegant icons for PyQT/PySide | https://pypi.org/project/QtAwesome/ | MIT |
pandas | Data analysis toolkit | https://pypi.org/project/pandas/ | BSD (BSD-3-Clause) |
numba | GPU acceleration of numpy ops | https://pypi.org/project/numba/ | BSD |
roifile | A library to read ImageJ ROIs | https://pypi.org/project/roifile/ | BSD 3-Clause |
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