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3dcell_tracking_dsaa2019

This repository contains the codes for the paper we submitted to IEEE DSAA 2019 : "Lightweight and Scalable Particle Tracking and Motion Clustering of 3D Cell Trajectories"

annotated-transformer

An annotated implementation of the Transformer paper.

ants

Advanced Normalization Tools (ANTs)

attention-is-all-you-need-pytorch

A PyTorch implementation of the Transformer model in "Attention is All You Need".

awesome-bci

Curated Collection of BCI resources

awesome-nerf

A curated list of awesome neural radiance fields papers

awesome-neural-rendering

A collection of resources on neural rendering.

brain-diffusion

Exploration of diffuison-based generative model to sychronizing brain dynamics from semantic language input.

brainrender

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

brian2

Brian is a free, open source simulator for spiking neural networks.

caiman

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

concurrent-and-distributed-computing-with-python

Concurrent and Distributed Computing with Python [video], published by Packt

cvapp-neuromorpho.org

Version of Cvapp as used on NeuroMorpho.org. Based on Robert Cannon's initial implementation.

dcimg

A Python module for accessing Hamamatsu DCIMG files

dcimg_to_tiff_conversion

deeplabcut

Official implementation of DeepLabCut: Markerless pose estimation of user-defined features with deep learning for all animals

deepops

Tools for building GPU clusters

dinov2

PyTorch code and models for the DINOv2 self-supervised learning method.

ffn

Flood-Filling Networks for instance segmentation in 3d volumes.

fish

Tools for working with zebrafish data generated by the Ahrens lab at Janelia Research Campus

ipyparaview

iPython widget for server-side ParaView rendering in Jupyter.

l-measure

3D Neuronal morphology analytical tool for deriving geometrical and topological statistics of digital neuronal reconstructions

machine-learning-articles

🧠💬 Articles I wrote about machine learning, archived from MachineCurve.com.

magpie

Magpie contains a number of scripts for running Big Data software in HPC environments, including Hadoop and Spark. There is support for Lustre, Slurm, Moab, Torque. LSF, and more.

mastering-concurrency-in-python

Mastering Concurrency in Python, published by Packt

mayavi

3D visualization of scientific data in Python

moving-zebrafish-larvae-segmentation-and-tracking-dataset-

Moving zebrafish larvae segmentation dataset consisting original video frames and their manually segmented ground truth or golden standard of the moving zebrafish larvae in each frame, as well as a region based segmentation accuracy evaluation program written in MATLAB.

nanogpt

The simplest, fastest repository for training/finetuning medium-sized GPTs.

nat

NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.

nerds

:angel: Matlab package implementing blind deconvolution method for neural spike recovery