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Thomas's Projects

brainrender icon brainrender

a python based software for visualization of neuroanatomical and morphological data.

caiman icon caiman

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

cellsort icon cellsort

This toolbox includes routines for using principal component analysis (PCA) and independent component analysis (ICA) to extract cellular signals from imaging data sets. A full description and validation of the method is provided in the paper, "Automated Analysis of Cellular Signals from Large-Scale Calcium Imaging Data," Neuron, 63:747 (2009): http://tinyurl.com/cellsort

lipidcreator icon lipidcreator

LipidCreator is a powerful stand alone kick-off tool for targeted lipidomics and a plugin for Skyline. It provides convenient tools to generate transition lists for labeled and unlabeled lipids.

nanocamera icon nanocamera

A simple to use camera interface for the Jetson Nano for working with USB and CSI cameras in Python.

nltools icon nltools

Python toolbox for analyzing imaging data

suite2p icon suite2p

cell detection in calcium imaging recordings

zerocostdl4mic icon zerocostdl4mic

ZeroCostDL4Mic: A Google Colab based no-cost toolbox to explore Deep-Learning in Microscopy

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