img_process

What is this repo for?

• the processing of preprocessed brain image data files for image registration
• the extraction and processing of segmented suite2p cell traces and spatial coordinates
• the extraction and processing of behavioural image data

What does this repo contain?

• Modules contain functions which for image processing and cell trace processing
• Accompanying ipynotebooks demonstrate how to use the modules

Modules

'admin_functions.py' - useful administrative functions useful

'extract.py' - extracts suite2p segmented cells and runs pre-processing on it - this includes extraction and denoising of ca2+ data, binarisation with hidden markov model, and normalisation

'order_functions.py' - functions for reading and splitting large tiffs into single tiffs

'plot.py' - plotting functions for the visualisation of

'registration.py' - functions for applying image registration to images and points, using ants library

Notebooks

'extract.ipynb' - extracting segmented cells and processing fluorescence traces

'registration.ipynb' - register segmented cells to brain atlas and label neurons

'suite.ipynb' - running suite2p from python

'extract_tail_angle.ipynb' - extraction of tail segment positions and plotting