Biafra Ahanonu

A-SOID. An active learning platform for expert-guided, data efficient discovery of behavior.

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

Sophia-Script-for-Windows. :zap: The most powerful open source tweaker on GitHub for fine-tuning Windows 10 & Windows 11

SophiApp. :zap: The most powerful open source tweaker on GitHub for fine-tuning Windows 10 & Windows 11

DeepLabCut-live-GUI. GUI to run DeepLabCut on live video feed

splat. WebGL 3D Gaussian Splat Viewer

supersplat-viewer. Viewer application for superspl.at

supersplat-viewer. User-friendly, high-performance viewer for 3D Gaussian splats

GaussianViewer. JavaScript

splatviz. Full python interactive 3D Gaussian Splatting viewer for real-time editing and analyzing.

ganviz. Render the output of 3DGS GANs and invert your own face captured from a webcam

valheim-server-docker. Valheim dedicated gameserver with automatic update, World backup, BepInEx and ValheimPlus mod support

steering-vectors. Steering vectors for transformer language models in Pytorch / Huggingface

DeepSeek-R1.

DeepSeek-V3. Python

AutoStereota. An open-source automated surgical instrument for microendoscope implantation

keypoint-moseq. Python

VAME. Variational Animal Motion Embedding - A tool for time series embedding and clustering

MotionMapper. Sample implementation of the MotionMapper behavioral analysis algorithms

simba. SimBA (Simple Behavioral Analysis), a pipeline and GUI for developing supervised behavioral classifiers

rastermap. a visualization method for neural data

anipose. 🐜🐀🐒🚶 A toolkit for robust markerless 3D pose estimation

AcinoSet. Camera calibration & 3D pose estimation tools for AcinoSet

plotnine. A Grammar of Graphics for Python

sam2. The repository provides code for running inference with the Meta Segment Anything Model 2 (SAM 2), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.

ActSort-public. ActSort is an active learning accelerated cell sorter tool for calcium imaging.

GetThermal. Cross-platform USB thermal camera viewer

purethermal1-firmware. Reference firmware for PureThermal 1 FLIR Lepton Dev Kit

DeepLabCut-live. SDK for running DeepLabCut on a live video stream

DeepLabCut-live-GUI. GUI to run DeepLabCut on live video feed

n5-ij. ImageJ convenience layer for N5

HDF5_Vibez. HDF5 plugin for ImageJ and Fiji.

n5-viewer. BigDataViewer-based tool for visualizing multichannel multiscale N5 datasets.

Adaptive-Optics. MATLAB code used in Thornton, M. A., et al., Long-term in vivo three-photon imaging reveals region-specific differences in healthy and regenerative oligodendrogenesis, Nature Neuroscience, 2024.

BEND. Benchmarking DNA Language Models on Biologically Meaningful Tasks

Interaction-Calculus. A programming language and model of computation that matches the optimal λ-calculus reduction algorithm perfectly.

Bend. A massively parallel, high-level programming language

Operant_Temp_Assay_V2. C++

publication-cold-sensation-without-touch. Code & data supporting academic publication "A novel method to selectively elicit cold sensations without touch" published at Journal of Methods Neuroscience

pyview. GUI + API for processing and visualizing Calcium imaging data. Largely based on the IDL software "VIEW" developed by Giovanni Galizia. Implemented in Python by Ajayrama Kumaraswamy

locaNMF. Pytorch implementation of LocaNMF

sima. Python package for analysis of dynamic fluorescence microscopy data

MGS-pipeline-distribution. Mouse Grimace Scale Binary Pain/No-Pain Predictor

matnwb. A Matlab interface for reading and writing NWB files

heat-diffusion. Python

act. Python

aloha. Python

ai-models-fourcastnetv2. Python

MATLAB-language-server. TypeScript

tensor-demo. A quickstart guide to tensor decomposition

pub-sourmpis2023-neurips. Jupyter Notebook

napari-chatgpt. A napari plugin to process and analyse images with chatGPT!

llms-with-matlab. Connect MATLAB to LLM APIs, including OpenAI® Chat Completions, Azure® OpenAI Services, and Ollama™

Fooocus. Focus on prompting and generating

gradio. Build and share delightful machine learning apps, all in Python. 🌟 Star to support our work!

stable-diffusion-webui. Stable Diffusion web UI

projectsandcastle. Supporting tools for Android/Linux on the iPhone

tensortools. A very simple and barebones tensor decomposition library for CP decomposition a.k.a. PARAFAC a.k.a. TCA

mouse-pose-analysis. C++

CDB90. CDB90 battle dataset

Saleae_Output_Parser. A Python script that parsers Saleae Logic 2 output files into useful data sets.

Currentscape. Currentscape is a Python tool enabling scientists to easily plot the currents in electrical neuron models. The code is based on the paper Alonso and Marder, 2019.

generative_agents. Generative Agents: Interactive Simulacra of Human Behavior

lussac. Package for automatic post-processing and merging of multiple spike-sorting analyses.

CellExplorer. CellExplorer is a graphical user interface, a standardized processing module and data structure for exploring and classifying single cells acquired using extracellular electrodes.

ecephys_spike_sorting. Modules for processing extracellular electrophysiology data from Neuropixels probes

SRDTrans. SRDTrans: Spatial redundancy transformer for self-supervised fluorescence image denoising

Segment2P. Automated segmentation of micrographs containing fluorescent cell soma

carignan. Python

pytorch-CycleGAN-and-pix2pix. Image-to-Image Translation in PyTorch

labelImg. LabelImg is now part of the Label Studio community. The popular image annotation tool created by Tzutalin is no longer actively being developed, but you can check out Label Studio, the open source data labeling tool for images, text, hypertext, audio, video and time-series data.

NeuroSeg2. The related code of NeuroSeg2.

AmadeusGPT. We turn natural language descriptions of behaviors into machine-executable code

zenodo_get. Zenodo_get - a downloader for Zenodo records

bCNC. GRBL CNC command sender, autoleveler and g-code editor

Scratch-AID. Jupyter Notebook

harmonized_atlas. Code used to construct and annotate the harmonized reference atlas

PdfGptIndexer. RAG based tool for indexing and searching PDF text data using OpenAI API and FAISS (Facebook AI Similarity Search) index, designed for rapid information retrieval and superior search accuracy.

Fee-Scopes. documentation on lightweight head-mounted microscopes developed in the Fee Lab

dafny. Dafny is a verification-aware programming language

SorterHunter. An evolutionary approach to find small and low latency sorting networks

SEUDO. MATLAB

GraFT-analysis. This repository contains code for morphology-free analysis of functional fluorescence microscopy. The focal algorithm, Graph-Filtered Time-trace (GraFT) Dictionary Learning, is published in Charles et al. 2022 in the IEEE Transactions of Image Processing.

DISCo. Python

CaliAli. Calcium imaging inter-session alignment

Prompt-Segment-Anything. This is an implementation of zero-shot instance segmentation using Segment Anything.

BKinD. Behavioral Keypoint Discovery

PaCMAP. PaCMAP: Large-scale Dimension Reduction Technique Preserving Both Global and Local Structure

EditAnything. Edit anything in images powered by segment-anything, ControlNet, StableDiffusion, etc. (ACM MM)

ChronicPain2023_NatNeuro. code related to Shirvalkar et al. 2023 - Nature Neuroscience

deepcell-label. Cloud-based data annotation tools for biological images

lightning-sam. Fine-tune Segment-Anything Model with Lightning Fabric.

sahi. Framework agnostic sliced/tiled inference + interactive ui + error analysis plots

segment-anything-video. MetaSeg: Packaged version of the Segment Anything repository

Segment-and-Track-Anything. An open-source project dedicated to tracking and segmenting any objects in videos, either automatically or interactively. The primary algorithms utilized include the Segment Anything Model (SAM) for key-frame segmentation and Associating Objects with Transformers (AOT) for efficient tracking and propagation purposes.

segment-anything. The repository provides code for running inference with the SegmentAnything Model (SAM), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.

Perspective_Julia_for_Biologists. Online material for the Perspective: "Julia for Biologists" presented at JuliaCon 2021: https://www.youtube.com/watch?v=gRj7E5kYG1I

deepflash2. A deep-learning pipeline for segmentation of ambiguous microscopic images.

arxiv-latex-cleaner. arXiv LaTeX Cleaner: Easily clean the LaTeX code of your paper to submit to arXiv

dlcpr. toolkit for processing tracking data from DeepLabCut

DLCAnalyzer. R Scripts to analyze deep lab cut point data and related data

IntanToNWB. Convert Intan (rhd or rhs) files to NWB file format

palmreader. Jupyter Notebook

ANTs. Advanced Normalization Tools (ANTs)

flow_registration. Flow-Registration toolbox for 2P motion compensation

FIt-SNE. Fast Fourier Transform-accelerated Interpolation-based t-SNE (FIt-SNE)

modisfast. Fast and efficient access to MODIS, VIIRS and GPM Earth Observation data with R

blackmaRble. blackmaRble: retrieve, wrangle and plot VIIRS Black Marble nighttimelight data in R

pyimagej. Use ImageJ from Python

instant-ngp. Instant neural graphics primitives: lightning fast NeRF and more

nerf. Code release for NeRF (Neural Radiance Fields)

Geographical-Adventures. C#

SeqSeek_Classify_Data. Repository of publicly available data small enough to fit in github

striatum2P. Code and sample data used to generate figures in Badimon et al., 2020

bioformats. Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.

cisnecode.github.io. HTML

Kilosort. Fast spike sorting with drift correction

Pinpoint. Multi-probe trajectory planning in an intuitive 3D environment

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

inscopix-cnmfe. Algorithm for automated source extraction from 1P data

ROIMatchPub. Match suite2p ROIs between imaging sessions

MINI2P_toolbox. The codes, software, models, protocols, and etc. for building and using MINI2P to do the freely-moving recording and analysis. More details can be found in the original paper "Large-scale two-photon calcium imaging in freely moving mice(2021)".

aizynthfinder. A tool for retrosynthetic planning

JRCLUST. JRCLUST

vectorseq. Virally Encoded Connectivity Transgenic Overlay RNA sequencing (VECTORseq) defines projection neurons involved in sensorimotor integration.

DP-Lick-Detector. Distribution Package for Dual Port Lick Detector

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

Fast_Tiff_Write. A fast multi-image tiff writer for Matlab

Miniscope-LFOV. Large field-of-view miniature microscope for rats and larger animals.

DoubletDetection. Doublet detection in single-cell RNA-seq data.

DiaNN. DIA-NN - a universal automated software suite for DIA proteomics data analysis.

SpinalJ. Zuckerman Institute scripts for spinal cord analysis

causalpath. A project for exploring differentially active signaling paths related to proteomics datasets

MVG-CNN. Codes related to paper "Automated sleep stage classification of wide-field calcium imaging data via multiplex visibility graphs and deep learning"

matlab_motion_correct. Matlab code for post-hoc motion correction. Some rely on mex files in mex_tools.

PatchWarp. Image processing pipeline to correct motion artifacts and complex image distortions in neuronal calcium imaging data.

FIBSI_program. Associated with XXXX publication

FIOLA. Python

SpectralSegmentation. Open source ca imaging processing tools to aquire neural traces from 2 photon image sequences

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

DeepCAD. DeepCAD: Deep self-supervised learning for calcium imaging denoising

WaterDetect. Water Detect Algorithm

CellProfiler. An open-source application for biological image analysis

Cascade. Calibrated inference of spiking from calcium ΔF/F data using deep networks

CaPTure. Ca

BEAR. Official code for BEAR. "Efficient neural network approximation of robust PCA for automated analysis of calcium imaging data", MICCAI 2021.

invesalius3. 3D medical imaging reconstruction software

diaproteomics. Automated quantitative analysis of DIA proteomics mass spectrometry measurements.

pycro-manager. Python control of micro-manager for customized data acquisition

cnpy. library to read/write .npy and .npz files in C/C++

cellpose-napari. napari plugin for cellpose (see www.cellpose.org) - an anatomical segmentation tool

npy-matlab. Experimental code to read/write NumPy .NPY files in MATLAB

eulerr. Area-Proportional Euler and Venn Diagrams with Ellipses

Inflammation-Index. Repo for Inflammation Index Package for R Code

napari. napari: a fast, interactive, multi-dimensional image viewer for python

.github. Automate your workflows with GitHub actions for MATLAB.

gramm. Gramm is a complete data visualization toolbox for Matlab. It provides an easy to use and high-level interface to produce publication-quality plots of complex data with varied statistical visualizations. Gramm is inspired by R's ggplot2 library.

winget-cli. WinGet is the Windows Package Manager. This project includes a CLI (Command Line Interface), PowerShell modules, and a COM (Component Object Model) API (Application Programming Interface).

terminal. The new Windows Terminal and the original Windows console host, all in the same place!

macos-virtualbox. Push-button installer of macOS Catalina, Mojave, and High Sierra guests in Virtualbox on x86 CPUs for Windows, Linux, and macOS

minian. miniscope analysis pipeline with interactive visualizations

imagej-matlab. MATLAB integration with ImageJ data structures and runtime.

sublime_text. Issue tracker for Sublime Text

Up.Down.Method. R

oir2stdData. MATLAB script for converting Olympus .oir image files into MATLAB readable images and metadata

m2html. M2HTML: Documentation System for MATLAB and Octave

RayTracing. Simple ray tracing library in Python for optical design that considers simple optical elements (with ABCD ray matrices) but also finite diameters of elements to calculate aperture and field stops, field of view, etc... Useful to validate the design of an optical system (lenses positions, power and diameters). Also permits the propagation of gaussian laser beams through the same elements.

ggbiplot. A biplot based on ggplot2

Protter. a customizable protein feature visualization tool

tryCatchLog. R package for better error handling incl. logging with a full (!) stack trace incl. line numbers, post-mortem analysis and support for parallel processing

artMS. Analytical R Tools for Mass Spectrometry

MSstats. R package - MSstats

core. An Emacs framework for the stubborn martian hacker

vscode. Visual Studio Code

desktop. Focus on what matters instead of fighting with Git.

Brain-Observatory-Toolbox. A MATLAB toolbox for interacting with the Allen Brain Observatory

AutoMatlab. Sublime Text plugin with autocompletion, documentation generation and a command panel for Matlab.

ggplot2. An implementation of the Grammar of Graphics in R

MIST. Microscopy Image Stitching Tool

B-SOID. Behavioral segmentation of open field in DeepLabCut, or B-SOID ("B-side"), is a pipeline that pairs unsupervised pattern recognition with supervised classification to achieve fast predictions of behaviors that are not predefined by users.

bp_utils. A collection of scripts/source files that may be useful to others

EXTRACT-public. EXTRACT is a tractable and robust automated cell extraction tool for calcium imaging, which extracts the activities of cells as time series from both one-photon and two-photon calcium imaging movies.

Specter. Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics

OpenMS. The codebase of the OpenMS project

datajoint-matlab. Relational data pipelines for the science lab

warping. HTML

UpSetR. An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..

MediaInfo. Convenient unified display of the most relevant technical and tag data for video and audio files.

microsoft-r-open. Microsoft R Open Source

DeepDIA. Using deep learning to generate in silico spectral libraries for data-independent acquisition analysis.

openage. Clone of the Age of Empires II engine 🚀

Signal-Android. A private messenger for Android.

kiosk-console. DeepCell Kiosk Distribution for Kubernetes on GKE and AWS

trex. TRex, a fast multi-animal tracking system with markerless identification, and 2D estimation of posture and visual fields.

CAPTURE_demo. Demo code for CAPTURE and DANNCE

youtube-dl. Command-line program to download videos from YouTube.com and other video sites

tdw. ThreeDWorld simulation environment

FizzBuzzEnterpriseEdition. FizzBuzz Enterprise Edition is a no-nonsense implementation of FizzBuzz made by serious businessmen for serious business purposes.

bonsai. The compiler, IDE, and standard library for the Bonsai visual programming language for reactive systems

deepinterpolation. Python