- PGBAR
C++ software for spike inference from calcium imaging data. This software uses a sequential Monte Carlo strategy to infer spiking events from calcium imaging data. The approach is based on my recent work published on eLife.
- BINE
C++ software for neuronal ensemble identification. This data analysis program allows to extract groups of synchronously active neurons from data provided by the user in the form of a binary table. The statistical analysis is based on Diana et al, PLoS comp. bio. 2019 and it provides a Markov Chain Monte Carlo sampler of neuronal ensemble features such as the level of noise and synchrony among ensembles.
- neuroshed
C++/openCV image processing software for segmentation and cell labeling of 3D fluorescence imaging stacks.
- IntegratedOmics
C++/OpenGL force-based simulator for network visualization. The github respository hosts a JavaScript dynamic plot of the network.
- pysam
Python implementation of different Monte Carlo sampplers for Bayesian inference.
- rec2track
C++/openCV software for fast video acquisition and recording using PointGrey high-speed (450Hz) infrared cameras. The software is used to track fast movement of zebrafish tails during behavioral asseys.
- NeuroTools
C++/openCV toolbox for analysing large-scale neuronal population. The program implements several algorithms used in the comminity to process 2D fluorescence imaging data, including density-based cluster analysis and singular value decomposition.