65 projects
brainglobe
Python-based tools for computational neuroanatomy.
brainrender
Visualisation and exploration of brain atlases and other anatomical data
brainglobe-atlasapi
A lightweight python module to interact with and generate atlases for systems neuroscience.
brainrender-napari
A napari plugin to render BrainGlobe atlases and associated data as layers.
oscar-colony
A python package for breeding calculations.
poseinterface
A framework for benchmarking pose estimation and point tracking methods on animal beheviour videos.
datashuttle
DataShuttle automates the creation, validation and transfer of neuroscience project folders.
brainglobe-utils
Shared general purpose tools for the BrainGlobe project
movement
A Python toolbox for analysing animal body movements across space and time
cellfinder
Automated 3D cell detection in large microscopy images
driftplots
Interactively visualise Kilosort drift maps for checking inter-session alignment.
brainreg
Automated multi-atlas whole-brain microscopy registration
brainglobe-napari-io
Read and write files from the BrainGlobe computational neuroanatomy suite into napari
morphapi
A lightweight python package to download neuronal morphologies
ethology
Data processing tools for animal behavioural analysis
spikewrap
Run extracellular electrophysiology analysis with SpikeInterface
brainglobe-registration
A napari plugin for registration to a BrainGlobe atlas.
brainglobe-workflows
A collection of end-to-end data analysis workflows executed using BrainGlobe tools.
fancylog
Fancier logging in Python
brainglobe-template-builder
Build unbiased anatomical templates from individual images
derotation
Derotate multiphoton calcium imaging movies
photon-mosaic
Automating calcium imaging analysis
beekeeping
Manage video metadata for animal behaviour experiments
suite2p-NIU
Pipeline for calcium imaging (fork of the original suite2p)
brainglobe-segmentation
Segmentation of anatomical structures in a common coordinate space
brainglobe-heatmap
Rendering anatomical heatmaps with brainrender and matplotlib
slurmio
Python tools to read SLURM job parameters
qt-niu
Reusable Qt elements
brainglobe-space
Anatomical space conventions made easy
brainglobe-stitch
A tool to stich large tiled datasets generated by the mesoSPIM.
brainglobe-ccf-translator
a package to translate data between common coordinate frameworks
NeuralPlayground
The standardised environment for the hippocampus and entorhinal cortex models
openbioglobe
OpenBioGlobe
imio
Loading and saving of image data.
bg-atlasapi
A lightweight python module to interact with atlases for systems neuroscience
brainreg-napari
Multi-atlas whole-brain microscopy registration
cellfinder-napari
Efficient cell detection in large images
cellfinder-core
Automated 3D cell detection in large microscopy images
brainmapper
Whole brain cell detection and atlas registration
brainreg-segment
Manual segmentation of 3D brain structures in a common anatomical space
bgheatmap
Brain regions heatmaps in brainrender
WAZP
Wasp Animal-tracking Zoo project with Pose estimation
cellshape-cluster
3D shape analysis using deep learning
cellshape-cloud
3D cell shape analysis using geometric deep learning on point clouds
cellfinder-visualize
Cellfinder output visualization
python-packaging-at
Example of how to package Python projects
cellshape-voxel
3D shape analysis using deep learning
bg-space
Anatomical space conventions made easy
build-test-at
A simple Python package
slidebook-python
Open slidebook .sldy files in Python
synchro
Customisable file transfers using rsync
cordmap
imlib
General data processing functions
napari-brainreg-standard
Visualise brainreg registration output in standard space
brainio
Loading and saving of brain imaging data.
bgviewer
Visualisation and exploration of brain atlases
amap
Automated mouse atlas propagation
bgspace
Anatomical space conventions made easy
brainatlas-api
A lightweight python module to interact with atlases for systems neuroscience
spikey
Electrophysiology analysis
slicereg
Registration of 2D sections to a 3D volume
brainrender-test
Python scripts to use Allen Brain Map data for analysis and rendering
surfcut
Cutting confocal stacks at various depths relative to surface signal
cellfinder-analyst
Group level analysis of cellfinder results.
micrometa
Reading of microscopy metadata
