siddjakes's repositories
AcinoSet
Camera calibration & 3D pose estimation tools for AcinoSet
bonsai-osc-bidirectional-example
Sending data back and forth between bonsai and a pyqt python program via Osc
AnimateImages
Helper functions to make animations of images with corresponding traces and labels using matplotlib
zUMIs
zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
VAME
Variational Animal Motion Embedding
fishystuff
beta for binder
autopilot
Distributed behavioral experiments
hovercraft
Make dynamic impressive presentations from text files!
napari
napari: a fast, interactive, multi-dimensional image viewer for python
magicgui
build GUIs from python functions, using magic.
plugin-GUI
Software for processing, recording, and visualizing multichannel electrophysiology data
mousecam
A head-mounted camera system integrates detailed behavioral monitoring with multichannel electrophysiology in freely moving mice
mcp9600-python
Python library for the Pimoroni MCP9600 Thermocouple Amplifier Breakout
AllenSDK
code for reading and processing Allen Institute for Brain Science data
simba
SimBA (Simple Behavioral Analysis), a plug-and-play pipeline and GUI for developing supervised behavioral classifiers
anipose
🐜🐀🐒🚶 A full system for robust 3D markerless tracking
analysis-tools
Code for reading data saved by the Open Ephys GUI
ffmpeg-python
Python bindings for FFmpeg - with complex filtering support
CaImAn
Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.
suite2p
cell detection in calcium imaging recordings
FaceMap
matlab/python GUI for unsupervised video analysis of rodent behavior (capable of processing multiple camera views)
t-SNE
A Jupyter Notebook to explore the t-SNE visualization algorithm on a toy data set.
video_utils
Wrapper for OpenCV-Python's VideoCapture class. Supports pythonic indexing and slicing
miniscoPy
A package to analyse calcium imaging data recorded with the Miniscope.
ClearMap
ClearMap is a python toolbox for the analysis and registration of volumetric data from cleared tissues.
AntCam
Murthy Lab ant-tracking setup control code
PythonDeviceWrappers
Python Wrapper for Lab Devices