Pinned Repositories
AcinoSet
Camera calibration & 3D pose estimation tools for AcinoSet
AllenSDK
code for reading and processing Allen Institute for Brain Science data
analysis-tools
Code for reading data saved by the Open Ephys GUI
AnimateImages
Helper functions to make animations of images with corresponding traces and labels using matplotlib
anipose
🐜🐀🐒🚶 A full system for robust 3D markerless tracking
AntCam
Murthy Lab ant-tracking setup control code
arduino-control-panel
Electron App for interacting with my Arduino
autopilot
Distributed behavioral experiments
bonsai-osc-bidirectional-example
Sending data back and forth between bonsai and a pyqt python program via Osc
CaImAn
Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.
siddjakes's Repositories
siddjakes/AcinoSet
Camera calibration & 3D pose estimation tools for AcinoSet
siddjakes/AllenSDK
code for reading and processing Allen Institute for Brain Science data
siddjakes/analysis-tools
Code for reading data saved by the Open Ephys GUI
siddjakes/AnimateImages
Helper functions to make animations of images with corresponding traces and labels using matplotlib
siddjakes/anipose
🐜🐀🐒🚶 A full system for robust 3D markerless tracking
siddjakes/autopilot
Distributed behavioral experiments
siddjakes/bonsai-osc-bidirectional-example
Sending data back and forth between bonsai and a pyqt python program via Osc
siddjakes/CaImAn
Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.
siddjakes/ClearMap
ClearMap is a python toolbox for the analysis and registration of volumetric data from cleared tissues.
siddjakes/FaceMap
matlab/python GUI for unsupervised video analysis of rodent behavior (capable of processing multiple camera views)
siddjakes/ffmpeg-python
Python bindings for FFmpeg - with complex filtering support
siddjakes/fishystuff
beta for binder
siddjakes/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.
siddjakes/hovercraft
Make dynamic impressive presentations from text files!
siddjakes/Kalman-and-Bayesian-Filters-in-Python
Kalman Filter book using Jupyter Notebook. Focuses on building intuition and experience, not formal proofs. Includes Kalman filters,extended Kalman filters, unscented Kalman filters, particle filters, and more. All exercises include solutions.
siddjakes/magicgui
build GUIs from python functions, using magic.
siddjakes/mcp9600-python
Python library for the Pimoroni MCP9600 Thermocouple Amplifier Breakout
siddjakes/miniscoPy
A package to analyse calcium imaging data recorded with the Miniscope.
siddjakes/mousecam
A head-mounted camera system integrates detailed behavioral monitoring with multichannel electrophysiology in freely moving mice
siddjakes/napari
napari: a fast, interactive, multi-dimensional image viewer for python
siddjakes/plugin-GUI
Software for processing, recording, and visualizing multichannel electrophysiology data
siddjakes/simba
SimBA (Simple Behavioral Analysis), a plug-and-play pipeline and GUI for developing supervised behavioral classifiers
siddjakes/suite2p
cell detection in calcium imaging recordings
siddjakes/t-SNE
A Jupyter Notebook to explore the t-SNE visualization algorithm on a toy data set.
siddjakes/TeensyStep4
siddjakes/Test-oeps-GUI-plugin-dev-wshop
siddjakes/VAME
Variational Animal Motion Embedding
siddjakes/video_utils
Wrapper for OpenCV-Python's VideoCapture class. Supports pythonic indexing and slicing
siddjakes/VOTA-1
siddjakes/zUMIs
zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs