fucciphase 0.0.1

Cell cycle analysis plugin.

fucciphase

FUCCI cell cycle analysis plugin. Obtain cell cycle information from FUCCI fluorescence intensities.

Installation

The best way to run fucciphase is to install it in a virtual conda environment. Make sure that git is installed and can be called from the command line.

(SOON) To install from pip:

pip install fucciphase

If you wish to install it from source:

git clone https://github.com/Synthetic-Physiology-Lab/fucciphase
cd fucciphase
pip install -e .

The installation should not take longer than a few seconds (depending on your internet connection).

To use the notebooks, also install jupyter:

pip install jupyter

Usage

Fucci phase currently supports loading a TrackMate XML file:

from fucciphase import process_trackmate
from fucciphase.sensor import get_fuccisa_default_sensor

trackmate_xml = "path/to/trackmate.xml"
channel1 = "MEAN_INTENSITY_CH3"
channel2 = "MEAN_INTENSITY_CH4"

sensor = get_fuccisa_default_sensor()

df = process_trackmate(trackmate_xml,
                       channels=[channel1, channel2],
		       sensor=sensor,
                       thresholds=[0.1, 0.1])
print(df)

The TrackMate XML is converted to a Pandas DataFrame. Thus, in general data (e.g., stored in a CSV or XLSX file) that can be parsed into a DataFrame is supported.

Have a look at the examples in the example folder to get more information!

The runtime of the scripts depends on your datasize. 2D samples with a few hundred to a few thousand cells can be processed in a few minutes. Visualization in Napari can take a bit longer. Standard processing does not require a powerful computer. Make sure that you have sufficient RAM to load videos for visualization in Napari.

Development

To develop fucciphase, clone the repository, install fucciphase in your environment and install the pre-commit hooks:

git clone https://github.com/Synthetic-Physiology-Lab/fucciphase
cd fucciphase
pip install -e ".[test, dev]"
pre-commit install

If you want to build the documentation, replace the abovementioned pip install by:

pip install -e ".[test, dev, doc]"

Cite us

Di Sante, M., Pezzotti, M., Zimmermann, J., Enrico, A., Deschamps, J., Balmas, E., Becca, S., Solito, S., Reali, A., Bertero, A., Jug, F. and Pasqualini, F.S., 2025. CALIPERS: Cell cycle-aware live imaging for phenotyping experiments and regeneration studies. bioRxiv, https://doi.org/10.1101/2024.12.19.629259