BrightEyes-FFS
A toolbox for analysing Fluorescence Correlation Spectroscopy (FCS) and Fluorescence Fluctuation Spectroscopy (FFS) data with array detectors. The fcs module contains libraries for:
- Calculating autocorrelations and cross-correlations of raw FCS/FFS data (i.e. photon counts vs. time or photon arrival time traces). Supported file types include .h5, .ptu, and .czi.
- Fitting correlations to various 2D and 3D diffusion models
- Calibration-free FCS/FFS analysis such as circular-scanning FCS and pair-correlation analysis
- Miscellaneous tools
The fcs_gui module contains libraries for:
- Storing and loading FCS/FFS analysis sessions, as used in the GUI
The pch module contains libraries for:
- Calculating photon counting histograms
- Fitting histograms with Fluorescence Intensity Distribution Analysis (FIDA)
The tools module contains libraries for:
- Fitting various models to data (polynomial, Gaussian, power law, etc.)
- Stokes-Einstein relation
- Save/load 2D arrays to/from .csv files
- Save data to .tiff file
- Miscellaneous tools
Installation
You can install brighteyes-ffs via [pip] directly from [PyPI]:
pip install brighteyes-ffs
or using the version on GitHub:
pip install git+https://github.com/VicidominiLab/BrightEyes-FFS
It requires the following Python packages
h5py
joblib
matplotlib>=3.3.2
multipletau>=0.3.3
numpy>=1.19.4
pandas>=1.1.4
scipy
tifffile>=2020.9.29
seaborn
imutils
PyQt5
qdarkstyle
nbformat
ome_types
czifile
brighteyes_ism
notebook
ptufile
GUI
For quick and common types of analysis, you can use the GUI (https://github.com/VicidominiLab/BrightEyes-FFS-GUI), which contains most of the basic features. In addition, there is an automatic Jupyter Notebook writing tool to convert an analysis session started in the GUI to a Notebook.
License
Distributed under the terms of the [GNU GPL v3.0] license, "BrightEyes-FFS" is free and open source software
Contributing
You want to contribute? Great! Contributing works best if you creat a pull request with your changes.
- Fork the project.
- Create a branch for your feature:
git checkout -b my-new-feature - Commit your changes:
git commit -am 'My new feature' - Push to the branch:
git push origin my-new-feature - Submit a pull request!
1 maintainer
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Filter files by name, interpreter, ABI, and platform.
If you're not sure about the file name format, learn more about wheel file names.
Copy a direct link to the current filters
File details
Details for the file brighteyes_ffs-0.1.6.tar.gz.
File metadata
- Download URL: brighteyes_ffs-0.1.6.tar.gz
- Upload date:
- Size: 155.0 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via:
twine/6.1.0 CPython/3.10.7
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
c5aed25cda02f5e18848e9177d64559e46a72389e02ee0d3e6f02b6f790debe6
|
|
| MD5 |
4d151126b041bbb7bd54da92fddca565
|
|
| BLAKE2b-256 |
b85dba6e7209ba77e91cd2f141182dbf5b314ef365daad7458d37fe30c5be2b7
|
File details
Details for the file brighteyes_ffs-0.1.6-py3-none-any.whl.
File metadata
- Download URL: brighteyes_ffs-0.1.6-py3-none-any.whl
- Upload date:
- Size: 191.2 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via:
twine/6.1.0 CPython/3.10.7
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
07d43d37e70fce645b69d5d434b29428aea5cbdb914657f0ddceb90c739256db
|
|
| MD5 |
b75cb4bfc20dbe7e65eb76d2acbec2aa
|
|
| BLAKE2b-256 |
84f50a60231c5f00307d727f5e574a3e47c7b78c74be4eb7de4dcfee417797b1
|
