yz22015

obsidian-consistent-attachments-and-links

Obsidian plugin. Move note with attachments.

SNUB

track2p

Cell tracking for longitudinal calcium imaging recordings.

SUPPORT

Accurate denoising of voltage imaging data through statistically unbiased prediction, Nature Methods.

rastermap

a visualization method for neural data

ZETA

Zenith of Event-based Time-locked Anomalies

zetatest

Parameter-free statistical testing package

deepinterpolation

pywt

PyWavelets - Wavelet Transforms in Python

zetapy

Python code implementing the ZETA-test

openai_tools

Growing collection of scripts to summarize the scientific literature using large-language models like ChatGPT.

NeuTu

Software package for neuron reconstruction and visualization

PSID

Preferential Subspace Identification Algorithm

CEBRA

Learnable latent embeddings for joint behavioral and neural analysis - Official implementation of CEBRA

Pinpoint

Multi-probe trajectory planning in an intuitive 3D environment

pi2

C++ library and command-line software for processing and analysis of terabyte-scale volume images locally or on a computing cluster.

XrayAssistedStaining

Code for analyzing the heavy metal accumulation during X-ray assisted staining

napari-nD-annotator

DeepCAD-RT

DeepCAD-RT: Real-time denoising of fluorescence time-lapse imaging using deep self-supervised learning

The-Art-of-Linear-Algebra

Graphic notes on Gilbert Strang's "Linear Algebra for Everyone"

BSD

Blind Sparse Deconvolution for calcium imaging.

CaImAn

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

NoRMCorre

Matlab routines for online non-rigid motion correction of calcium imaging data

spikeinterface

A Python-based module for creating flexible and robust spike sorting pipelines.

NeuroPyxels

NeuroPyxels (npyx) is a python library built for electrophysiologists using Neuropixels electrodes. This package stems from the need of a pythonist who really did not want to transition to MATLAB to work with Neuropixels: it features a suite of core utility functions for loading, processing and plotting Neuropixels data.

pynapple

PYthon Neural Analysis Package :pineapple:

protocolBLAST

Sample preparation and warping accuracy for correlative multimodal imaging in the mouse olfactory bulb using two-photon, synchrotron X-ray and volume electron microscopy

warpAnnotations

A tool to transform annotations (such as points, skeletons or meshes) between spatial datasets.

suite2p

cell detection in calcium imaging recordings

elastix

Official elastix repository