pyfigures 0.1.3

PyFigures will assist you assemble publication ready scientific figures in no time.

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). Or click here to access the complete demo playlist.

NB: most demo images are from the cellimagelibrary.

Installation

1. Conda Installation (Advanced Users)

For advanced users, we recommend installing the software using Conda. This will offer unlimited scripting capabilities.

1. Install Miniconda (if not already present on your system)

2. 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

Note

• 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

2. Standalone Executable Installation (Easy)

Alternatively, you can install the software as a standalone executable. This does not require Conda and can be run on any system without the need for additional dependencies, but scripting capabilities will be limited to the bundled dependencies.

• Windows coming soon!
• MacOS coming soon!
• Linux coming soon!

Third party libraries

Below is a list of the 3^rd 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

Other Figure-Making Software

FigureJ

ScientiFig

omero.figure

EzFig

QuickFigures