MultifiberProcessing

MATLAB code to preprocess raw multifiber photometry data. This code was written and developed in MATLAB2020b. See Vu et al., 2024.

Main Steps

Note that each of these steps is packaged in a Matlab App. There are 2 ways to run each of these apps.

1. The .mlappinstall file contains the installer for the standalone app and includes the dependencies required.
2. If you have the dependencies required in your path (see below), you can alternatively just run the .mlapp file.

1) PREPROCESS_MULTIFIB

Convert raw movie files (.cxd) to 3D .tif files, and motion-correct. See PREPROCESS_MULTIFIB_README.pdf for instructions and more info.

2) MAP_ROIS

Establish ROIs and extract relevant neural data. See MAP_ROIS_README.pdf for instructions and more info.

Other useful functions included:

1. extract_ROI_timeseries.m
   • This is called by MAP_ROIS and also can be run as a standalone function to change the baseline window, or change the baseline calculation method (sliding 8th percentile vs exponential baseline).
   • Type 'help extract_ROI_timeseries' in the Matlab command window for more info.
2. motion_correct.m, load_tiffs_fast.m, and write_tiff_fast.m, functions originally provided by Dr. Jason R. Climer (jason.r.climer@gmail.com). Any updates have been noted within the script.

Dependencies

• Bio-Formats
• conv_fft2
• MATLAB Image Processing Toolbox
• MATLAB Statistics and Machine Learning Toolbox
• MATLAB Curve Fitting Toolbox

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License and Citation

If you use use this code in your research, please cite:

Vu MT, Brown EH, Wen MJ, Noggle CA, Zhang Z, Monk KJ, Bouabid S, Mroz L, Graham BM, Zhuo Y, Li Y, Otchy TM, Tian L, Davison IG, Boas DA, Howe MW. Targeted micro-fiber arrays for measuring and manipulating localized multi-scale neural dynamics over large, deep brain volumes during behavior. Neuron. 2024 Mar 20;112(6):909-923.e9..

This repository is released under the MIT License - see the LICENSE file for details.

Acknowledgements

This work was supported by Aligning Science Across Parkinson’s (ASAP-020370) through the Michael J. Fox Foundation for Parkinson’s Research (MJFF), National Institute of Mental Health (R01 MH125835), Whitehall Foundation Fellowship, Klingenstein-Simons Foundation Fellowship, and Parkinson’s Foundation (Stanley Fahn Junior Faculty Award, PF-SF-JFA-836662) to M.W.H.; NIMH F32MH120894 to M.-A.T.V.