fucciphase 0.0.1__py3-none-any.whl → 0.0.3__py3-none-any.whl

fucciphase-0.0.1.dist-info/METADATA

@@ -1,137 +0,0 @@
-Metadata-Version: 2.4
-Name: fucciphase
-Version: 0.0.1
-Summary: Cell cycle analysis plugin.
-Project-URL: homepage, https://github.com/nobias-ht/fucciphase
-Project-URL: repository, https://github.com/nobias-ht/fucciphase
-Author-email: Joran Deschamps <joran.deschamps@fht.org>
-License: BSD-3-Clause
-License-File: LICENSE
-Classifier: Development Status :: 3 - Alpha
-Classifier: License :: OSI Approved :: BSD License
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Requires-Python: >=3.8
-Requires-Dist: dtaidistance
-Requires-Dist: lineagetree<1.5.0
-Requires-Dist: matplotlib
-Requires-Dist: monotonic-derivative
-Requires-Dist: numpy
-Requires-Dist: openpyxl
-Requires-Dist: pandas
-Requires-Dist: scipy
-Requires-Dist: svgwrite
-Provides-Extra: dev
-Requires-Dist: ipython; extra == 'dev'
-Requires-Dist: mypy; extra == 'dev'
-Requires-Dist: pdbpp; extra == 'dev'
-Requires-Dist: pre-commit; extra == 'dev'
-Requires-Dist: rich; extra == 'dev'
-Requires-Dist: ruff; extra == 'dev'
-Provides-Extra: doc
-Requires-Dist: sphinx; extra == 'doc'
-Provides-Extra: jupyter
-Requires-Dist: jupyter; extra == 'jupyter'
-Provides-Extra: test
-Requires-Dist: pytest; extra == 'test'
-Requires-Dist: pytest-cov; extra == 'test'
-Description-Content-Type: text/markdown
-
-# fucciphase
-
-[![License](https://img.shields.io/pypi/l/fucciphase.svg?color=green)](https://github.com/Synthetic-Physiology-Lab/fucciphase/raw/main/LICENSE)
-[![PyPI](https://img.shields.io/pypi/v/fucciphase.svg?color=green)](https://pypi.org/project/fucciphase)
-[![Python Version](https://img.shields.io/pypi/pyversions/fucciphase.svg?color=green)](https://python.org)
-[![CI](https://github.com/Synthetic-Physiology-Lab/fucciphase/actions/workflows/ci.yml/badge.svg)](https://github.com/Synthetic-Physiology-Lab/fucciphase/actions/workflows/ci.yml)
-[![codecov](https://codecov.io/gh/Synthetic-Physiology-Lab/fucciphase/branch/main/graph/badge.svg)](https://codecov.io/gh/Synthetic-Physiology-Lab/fucciphase)
-[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/Synthetic-Physiology-Lab/fucciphase/main.svg)](https://results.pre-commit.ci/latest/github/Synthetic-Physiology-Lab/fucciphase/main)
-
-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:
-
-```bash
-pip install fucciphase
-```
-
-If you wish to install it from source:
-    
-```bash
-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:
-    
-```bash
-pip install jupyter
-```
-
-## Usage
-
-Fucci phase currently supports loading a 
-[TrackMate](https://imagej.net/plugins/trackmate/) XML file:
-
-```python
-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](https://pandas.pydata.org/) 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:
-
-```bash
-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:
-```bash
-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 

fucciphase-0.0.1.dist-info/RECORD

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-fucciphase-0.0.1.dist-info/RECORD,,