eLife Sciences's Projects
Code for post processing steps for BWTT acquired data (Romano et al. 2018)
CaCLEAN restores the Ca2+ release maps (or active CRUs) in beating cardiomyocytes.
Code for analyses reported in Cadwell et al., 2020
Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.
Complete Matlab pipeline for large scale calcium imaging data analysis
Code to reproduce figures in "A big-data approach to understanding metabolic rate and response to obesity in laboratory mice"
MATLAB script for calculating action potentials propagation velocities using spikes timestamps in specified electrodes in a MEA device (coupled with microfluidics)
Code for paper "Alternative stable states in a model of microbial community limited by multiple essential nutrients"
Code for pneumococcal carriage duration
plotting and fitting functions
Plugin for Blender to interface with CATMAID Server and Pull Data
Raw FACS data and analysis code for Cattoglio et al. 2019
conductance-based encoding model
Seunghee's project
Tools for clustering neurons using synaptic connectivity
Supplementary Data Submission eLife
Bayesian method to estimate embryonic age for mouse embryos.
data and visualization script accompanying eLife publication
GWA mapping with C. elegans
This python script allows the semi-automatic analysis of cell separations in 2D images, and can further perform comparisons of mean cell separation area between two conditions or genotypes, as well as the analysis of cell separation orientation and anisotropy of multiple conditions or genotypes.
Segmenting Escherichia coli cells in phase contrast images based on Otsu method to read the fluorescent intensity within the cells
scripts to track nuclei over time and measure mean intensity fluorescence levels
Code for generating trajectories of E coli swimming in microfluidic device
For automated or manual quantification of pERK/tERK values in individual cells from high-resolution images