lig2017

BoutonAnalyzer

BoutonAnalyzer is software for detection and tracking of structural changes in en passant boutons in time-lapse light-microscopy stacks of images, developed by the Neurogeometry lab.

CaImAn

Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.

CaImAn-MATLAB

Complete Matlab pipeline for large scale calcium imaging data analysis

cellAggregator

cellprofiler-practical-NeuBIAS-Lisbon-2017

CellTracker

scripts to track nuclei over time and measure mean intensity fluorescence levels

elife2018-dot_detection

FociFinder3D

freeCodeCamp

The https://freeCodeCamp.org open source codebase and curriculum. Learn to code for free together with millions of people.

ggally

R package that extends ggplot2

gphys

R package to analyse electrophysiology data acquired by Neuromatic / Igor Pro

haley_hampton_marder_2018

Analysis package for the paper Haley, Hampton, and Marder (2018)

kinesin-3_guedes-dias_2018

kinesin-3_guedes-dias_2018

kymo

matlab script to trace fluorescent particles in kymograph

lin_elife_2018_tCyCIF_plots

Jupyter Notebook for plotting single-cell data from Lin et al. 2018

Liu_et_al_2018_eLife

ImageJ macro for analyzing fluorescence lifetime images and CellProfiler pipeline for multi-channel colocalization analysis

markdown-portfolio

msdanalyzer

A MATLAB class for Mean Square Displacement analysis.

nuclear-fractionation

Partition nuclear and cytoplasmic compartments within a cellular ROI for measurement.

Omega

Open Microscopy Environment inteGrated Analysis (OMEGA) is a cross-platform data management, analysis and visualization system, for particle tracking data with particular emphasis on results from viral and vesicular trafficking experiments.

online.bioinformatics

pyfluo

A python library for Ca imaging data analysis.

QuantEvForTrackMate

radialitymap

Splitting image to radial and non-radial components ImageJ macro

rxivist

API providing access to papers and authors scraped from biorxiv.org

Single-vesicle-fusion-events

TraJ

Library for diffusion trajectory analysis