Fluorescence Python Packages

fretbursts

Burst analysis software for single and multi-spot single-molecule FRET (smFRET) data.

rosettax

Interactive flow cytometry calibration software for fluorescence and scattering workflows, with FCS loading, peak finding, fitting, profiles, and reusable calibration exports.

opticalmapping

An open-source python library for the processing of fluorescence video data

optimap

An open-source python library for the processing of fluorescence video data

labellib

Library for coarse-grained simulations of probes flexibly coupled to biomolecules.

cindra

Provides pipelines for processing neural imaging data and tracking Regions of Interest across multiple recordings.

flimkit-qupath-bridge

Direct image and ROI exchange between FLIMKit and QuPath

tttrlib

File format agnostic low level, high performance API to read and process time-tagged-time resolved (TTTR) data for single-molecule and image spectroscopy)

flika

An interactive image processing program for biologists written in Python.

corrct

Physically corrected projectors for X-ray induced emission CT.

papylio

Single-molecule fluorescence trace extraction and analysis

cytoflow

A Python toolbox for quantitative, reproducible flow cytometry analysis

lifefit

Analyze fluorescence lifetime and anisotropy decays.

icsdll

Interface to the image correlation spectroscopy library ICSx64.dll.

cellector

A pipeline and GUI for determining which ROIs match features in a fluorescence image.

nellie

Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy

ifpd

iFISH Probe Design: a Python3 package to build iFISH probes.

imswitch

ImSwitch is a software solution in Python that aims at generalizing microscope control by providing a solution for flexible control of multiple microscope modalities.

axoden

Open-source tool for unbiased quantification of labeled axonal projections from microscopy images. Fluorophore- and species-agnostic, using Otsu thresholding. Available as a web app, standalone GUI, and Python package.

smo

Robust and unbiased estimation of the background distribution for fluorescence microscopy.

calciumflexanalysis

Read and interpret calcium flux assays

hts-tools

🏮 Parsing and analysing platereader absorbance and fluorescence data.

pyeem

Python library for the preprocessing, correction, deconvolution and analysis of Excitation Emission Matrices (EEMs).

cytoself

Self-supervised models for encoding protein localization patterns from microscopy images