Targeted micro-fiber arrays for measuring and manipulating localized multi-scale neural dynamics over large, deep brain volumes during behavior: resources and main figure data

Summary:

Neural population dynamics relevant for behavior vary over multiple spatial and temporal scales across 3-dimensional volumes. Current optical approaches lack the spatial coverage and resolution necessary to measure and manipulate naturally occurring patterns of large-scale, distributed dynamics within and across deep brain regions such as the striatum. We designed a new micro-fiber array approach capable of chronically measuring and optogenetically manipulating local dynamics across over 100 targeted locations simultaneously in head-fixed and freely moving mice. We developed a semi-automated micro-CT based strategy to precisely localize positions of each optical fiber. This highly-customizable approach enables investigation of multi-scale spatial and temporal patterns of cell-type and neurotransmitter specific signals over arbitrary 3-D volumes at a spatial resolution and coverage previously inaccessible. We applied this method to resolve rapid dopamine release dynamics across the striatum volume which revealed distinct, modality specific spatiotemporal patterns in response to salient sensory stimuli extending over millimeters of tissue. Targeted optogenetics through our fiber arrays enabled flexible control of neural signaling on multiple spatial scales, better matching endogenous signaling patterns, and spatial localization of behavioral function across large circuits. 

Files included: 

• Vu, M-A. et al. (2023) - Key Resources Table.xlsx -- key resources used in this study
• README_figure_data_and_analysis.txt --a description of the organization of the files within this repository
• README_preprocessing_code.txt -- details about the preprocessing pipeline (including registration and localization pipelines) and annotation of the preprocessed data structure
• preprocessing_code.zip -- contains all the preprocessing code
• Fig01.zip -- preprocessed data and analysis code for main Figure 1
• Fig03.zip -- preprocessed data and analysis code for main Figure 3
• Fig04.zip -- preprocessed data and analysis code for main Figure 4
• Fig05.zip -- preprocessed data and analysis code for main Figure 5
• Fig06.zip -- preprocessed data and analysis code for main Figure 6
• Fig07.zip -- preprocessed data and analysis code for main Figure 7
• SuppFig01.zip -- preprocessed data and analysis code for supplemental Figure 1
• SuppFig02.zip -- preprocessed data and analysis code for supplemental Figure 2
• SuppFig03.zip -- preprocessed data and analysis code for supplemental Figure 3
• SuppFig04.zip -- preprocessed data and analysis code for supplemental Figure 4
• SuppFig05.zip -- preprocessed data and analysis code for supplemental Figure 5
• SuppFig06.zip -- preprocessed data and analysis code for supplemental Figure 6
• SuppFig07.zip -- preprocessed data and analysis code for supplemental Figure 7

Each .zip file contains a folder corresponding to a figure.  Within each figure folder will be a folder corresponding to the letter (e.g., A, B, C) of the panel within the figure. In addition to the panel folders, when applicable, there may also be a folder containing general-use functions or scripts, or interim results .mat files, that are called by the scripts within the subfolders. In each subfolder there will be 3 things:

1. a folder of preprocessed data (see README_preprocessing_code.txt)
2. a folder of the analysis scripts that analyzed the preprocessed data and generated the figure
3. a README text file detailing the contents of both folders and the analysis workflow.