cechava's repositories
2p-tester-scripts
tmp repo for testing analysis pipeline
acquisition-tools
tmp repo for various aspects of acquisition
Acquisition2P_class
For managing 2P imaging datasets from preprocessing to activity trace extraction
badges
:pencil: Markdown code for lots of small badges :ribbon: :pushpin: (shields.io, forthebadge.com etc) :sunglasses:. Contributions are welcome! Please add yours!
ca_source_extraction
Matlab implementation of a source extraction and spike inference algorithm for large scale calcium imaging data analysis, based on a constrained matrix factorization approach.
dann_tf2.0
DANN in TensorFlow 2.0
DeepLabCut
Markerless tracking of user-defined features with deep learning
EXTRACT-public
EXTRACT is a tractable and robust automated cell extraction tool for calcium imaging, which extracts the activities of cells as time series from both one-photon and two-photon calcium imaging movies.
FaceMap
matlab GUI for unsupervised video analysis of rodent behavior (capable of processing multiple camera views)
GCaMP
analysis scripts for GCaMP data
hdmf
The Hierarchical Data Modeling Framework
helperFunctions
Common functions that may be used by all other functions in the Harvey Lab code base.
matnwb
A Matlab interface for reading and writing NWB files
NoRMCorre
Matlab routines for online non-rigid motion correction of calcium imaging data
pynwb
A Python API for working with Neurodata stored in the NWB Format
roiextractors
Python-based module for extracting from, converting between, and handling recorded and optical imaging data from several file format. Inspired by SpikeExtractor
steinmetz-et-al-2019
Code accompanying Steinmetz et al., 2019
suite2p
cell detection in calcium imaging recordings
tf-dann
Domain-Adversarial Neural Network in Tensorflow