tzklab / carignan

Carignan: Calcium real-time imaging for graphical network analysis of neurons

Real-time calucium imaging software based on CaImAn.

• frame-by-frame OnACID with simple GUI
  • works on Windows, Mac or Linux
  • false-positive neuron detector based on CNMF-E Reviewer
    • Issue: automl model cannot use in Windows
• real-time detection of synchronous firing of neurons
• laser handling module to interfere with mouse neurons

system overview: https://docs.google.com/presentation/d/1JQzA2FbH6-Qm684_ZjaZ5lzTnqpJ5fwVmMV1iSqYTr8

Setup

please set Python to version 3.7 before runnning below

python -V # >> 3.7.0

# Mac / Linux
source setup.sh

# Windows
setup.ps1

• Download data.zip from here and unzip.
• Download .npy files to data/cnmfe-reviewer/ from here.

Run

# from miniscope
python main.py -s

# from video file
python main.py -f