World Wide Series Seminar Kilosort is a software package for identifying neurons and their spikes in extracellular electrophysiology, a process known as “spike sorting”. Kilosort has been primarily developed and tested on the Neuropixels 1.
World Wide Series Seminar Suite2P is a very modular imaging processing pipeline written in Python which allows you to perform registration of raw data movies, automatic cell detection, extraction of calcium traces and infers spike times.
The BigPint package can help examine any large multivariate dataset. However, we note that the example datasets and example code in this package consider RNA-sequencing datasets. If you are using this software for RNA-sequencing data, then it can help you confirm that the variability between your treatment groups is larger than that between your replicates and determine how various normalization techniques in popular RNA-sequencing analysis packages (such as edgeR, DESeq2, and limma) affect your dataset.
COINSTAC provides a platform to analyze data stored locally across multiple organizations without the need for pooling the data at any point during the analysis. It is intended to be an ultimate one-stop shop by which researchers can build any statistical or machine learning model collaboratively in a decentralized fashion.
This workflow is used to analyze large-scale, multi-round, high-resolution image data acquired using EASI-FISH (Expansion-Assisted Iterative Fluorescence In Situ Hybridization). It takes advantage of the n5 filesystem to allow for rapid and parallel data reading and writing.
MNE-Python is an open-source Python module for neuroscience data analysis. It implements many neuroscience-specific algorithms and statistical tools; has rich visualization capabilities that are both interactive and fully scriptable (for reproducibility); and integrates easily with general-purpose libraries like SciPy, Scikit-learn, and TensorFlow.
Napari is a fast, interactive, multi-dimensional image viewer for Python. It’s designed for browsing, annotating, and analyzing large multi-dimensional images. It’s built on top of Qt (for the GUI), vispy (for performant GPU-based rendering), and the scientific Python stack (numpy, scipy).
CLIJ2 is a GPU-accelerated image processing library for ImageJ/Fiji, Icy, Matlab and Java based on OpenCL. It comes with hundreds of operations for filtering, binarizing, labeling, measuring in images, projections, transformations and mathematical operations for images.
morphologica is a header-only C++ library which provides simulation support facilities for simulations of dynamical systems.
It helps with:
Configuration: morphologica allows you to easily set up a simulation parameter configuration system, using the JSON reading and writing abilities of morph::Config.
NetPyNE (Networks using Python and NEURON) is a Python package to facilitate the development, simulation, parallelization, analysis, and optimization of biophysical neuronal networks using the NEURON simulator.
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