A list of software and hardware currently used within IBL
 

 Basic setup for mice to perform a perceptual decision-making task

Basic setup for mice to perform a perceptual decision-making task

Paper initially using rig:
https://doi.org/10.1016/j.celrep.2017.08.047

Rig-building instructions:
https://www.ucl.ac.uk/cortexlab/tools/wheel

New controllers (Bpod modules):
https://sanworks.io/
https://github.com/sanworks/Bpod_Gen2

Python User Interface for experimental control (PyBpod):
https://github.com/int-brain-lab/pybpod

IBL githhub:
https://www.github.com/int-brain-lab

Data managed in Alyx:
https://alyx.readthedocs.io/en/latest/index.html

Data saved as .alf:
 https://github.com/cortex-lab/alf2neuroscope#what-is-alf

Potentially useful software

Some recent relevant references

Neural data science: accelerating the experiment-analysis-theory cycle in large-scale neuroscience; Liam Paninski, John Cunningham
https://www.biorxiv.org/content/early/2017/10/02/196949

Data types

Calcium+voltage imaging:

https://github.com/flatironinstitute/CaImAn
https://github.com/zhoupc/CNMF_E
https://github.com/cortex-lab/Suite2P
https://github.com/jewellsean/FastLZeroSpikeInference
https://github.com/losonczylab/sima

Multi-electrode recordings (spike sorting):

https://github.com/cortex-lab/KiloSort
http://www.jrclust.org/
https://github.com/paninski-lab/yass
https://github.com/flatironinstitute/mountainsort
https://github.com/pillowlab/BinaryPursuitSpikeSorting

Multi-electrode recordings (online processing and closed-loop control):

https://github.com/open-ephys/plugin-GUI

Local field potentials

Intracellular recording

http://neuralensemble.org/neo/

Optogenetic stimulation


matlab tools for SLM targeting and hologram generation
https://github.com/wjyangGithub/Holographic-Photostimulation-System  

Structural Images (optical)

Behavioral + stimulus control (and analysis)

http://www.open-ephys.org/bonsai/
http://www.openmaze.org/
https://pni.princeton.edu/pni-software-tools/virmen
https://github.com/dendritic/signals

Electron microscopy

WebGL-based viewer for volumetric data
https://github.com/google/neuroglancer

For working with "precomputed" format of Neuroglancer
https://github.com/seung-lab/cloud-volume

Aligning images of serial sections
https://github.com/seung-lab/Alembic

Spike train data analysis methods - encoding models, decoders, dimensionality reduction, etc

Registration + visualization of multi-modal imaging datasets
http://www.simpleitk.org/
https://github.com/neurodata/ndreg
http://stnava.github.io/ANTs/
https://github.com/khaledkhairy/EM_aligner
http://xarray.pydata.org/en/stable/

RF estimation (ASD prior)
https://github.com/pillowlab/fastASD

GLM fitting for trial-based data
https://github.com/pillowlab/neuroGLM

Entropy Estimation
https://github.com/pillowlab/CDMentropy/

Compression of large video data
http://blosc.org/
https://bellard.org/bpg/

Eye tracking
https://github.com/AllenInstitute/allensdk.eye_tracking
https://github.com/kristinbranson/APT  (private repo, access available on request)
https://github.com/mkrumin/EyeTracking
https://github.com/carsen-stringer/FaceMap

Animal part tracking
https://github.com/kristinbranson/APT
http://ilastik.org/
https://github.com/AlexEMG/DeepLabCut
https://github.com/carsen-stringer/FaceMap

Visualization (2scRNAseq / FISHD, 3D, 4D, 5D)

Web-Viz
http://catmaid.readthedocs.io/en/stable/
https://github.com/google/neuroglancer
https://github.com/neurodata/ndviz
http://www.geppetto.org/

Local Viz
https://imagej.net/BigDataViewer
http://www.alleninstitute.org/what-we-do/brain-science/research/products-tools/vaa3d/

Pipelines, data sharing, reproducibility

Tracking provenance of data / analysis outputs.  Automatic repopulation of databases as analysis algorithms are updated. Store both data and model simulation output
https://datajoint.github.io/

Data specifications
https://neurodatawithoutborders.github.io/
http://bids.neuroimaging.io/

Reproducibility + sharing tools
https://mybinder.org/
http://gigantum.io/
https://colab.research.google.com/notebooks/welcome.ipynb
https://www.kaggle.com/kernels

Data/Tool Repositories
https://crcns.org/
https://neurodata.io/
https://www.nitrc.org/
http://datalad.org/