links to key resources for data acquisition and analysis
https://github.com/SjulsonLab/methods_class
https://www.neuropixels.org/support SpikeGLX (recommended) https://github.com/billkarsh/SpikeGLX openEphys
https://neuropixelsgroup.slack.com https://github.com/cortex-lab/neuropixels/wiki http://billkarsh.github.io/SpikeGLX/
https://github.com/cortex-lab/neuropixels/wiki/Other_analysis_methods
probe holder https://gitlab.com/OptogeneticsandNeuralEngineeringCore/neuropixels probe sharpening https://github.com/cortex-lab/neuropixels/wiki/Probe-Sharpening
- fluoroSNAPP
- suite2p https://github.com/MouseLand/suite2p
- CaiMan https://github.com/flatironinstitute/CaImAn
- Mesmerize https://github.com/kushalkolar/MESmerize http://www.mesmerizelab.org/Overview.html
- kilosort2 https://github.com/MouseLand/Kilosort2
- Neural decoding (Kording lab - user friendly) https://arxiv.org/abs/1708.00909 https://github.com/kordingLab/neural_decoding
- kilosort2: https://www.janelia.org/lab/pachitariu-lab/talks
- DeepInsigth https://www.biorxiv.org/content/10.1101/871848v1 https://github.com/CYHSM/DeepInsight
- Bonsai (ephys and behavior stream - visual programming https://bonsai-rx.org/
- DeepLabCut https://github.com/AlexEMG/DeepLabCut https://github.com/MMathisLab/Docker4DeepLabCut2.0 https://github.com/sgoldenlab/simba - GUI
- DLC tools (ROI tool with DLC) https://github.com/PolarBean/DLC_ROI_tool
- Loopbio http://loopbio.com/ https://github.com/loopbio
- 3D pose estimation http://anipose.org/
- Facemap https://github.com/MouseLand/FaceMap
- Whiskers whisk locoWhisk https://www.sciencedirect.com/science/article/pii/S0165027019302973
- B-SOID from deeplabcut to b-soid for classification of behavior https://github.com/YttriLab/B-SOID article https://www.biorxiv.org/content/biorxiv/early/2019/09/16/770271.full.pdf how to video and notes https://github.com/wAOndering/Meeting_notes
- VAME https://www.biorxiv.org/content/10.1101/2020.05.14.095430v1.full.pdf https://github.com/LINCellularNeuroscience/VAME
- SimBA https://github.com/sgoldenlab/simba
- Motion mapper https://github.com/gordonberman/MotionMapper
- DeepSqueak - rat (https://www.nature.com/articles/s41386-018-0303-6)
- VocalMat - mouse (https://twitter.com/dietrich_mo/status/1264995874767339524?s=20) (repo https://github.com/ahof1704/VocalMat) Social 3D https://www.biorxiv.org/content/10.1101/2020.05.21.109629v1 Virus Addgene info and feedback on viruses https://datahub.addgene.org/aav/
- EyeLoop https://github.com/simonarvin/eyeloop
- with DLC DeepLabStream - https://github.com/SchwarzNeuroconLab/DeepLabStream
- with DLC Bonsai https://github.com/bonsai-rx/deeplabcut#bonsai---deeplabcut
- with DLC https://www.eneuro.org/content/7/3/ENEURO.0485-19.2020 and openMV https://openmv.io/pages/download
- Pixycam https://pixycam.com/
https://github.com/cortex-lab/mmmGUI https://github.com/AdaptiveMotorControlLab/Camera_Control