Doric Fiber Photometry Data Analysis

This project provides a complete workflow for processing and analyzing data from fiber photometry experiments using Doric files in HDF5 format. The analysis is structured around three different tasks: "Stim," "CS," and "Knob," with results visualized in a variety of formats.

Project Overview

This project aims to process, analyze, and visualize fiber photometry data, producing comprehensive insights into experimental results. It provides:

• Data Processing: Handling various formats, including CSV and HDF5, processing them into usable forms.
• Data Analysis: Generating PSTH (Peri-Stimulus Time Histogram) data, confidence intervals, and other statistical measures.
• Visualization: Creating bar charts, heatmaps, and other visualizations for raw and processed data.

Installation Instructions

1. Clone the Repository:

   git clone <repository_url>
   cd FiberPhotometryDataAnalysis

2. Install Dependencies:

   The project requires various Python packages. Install them using:

   pip install -r requirements.txt

3. Data Setup:

   Ensure you have your experimental data organized in a folder structure similar to the one described in the project.

Walkthrough: Jupyter Notebooks

1. CS-doric-psth.ipynb

• Data Loading: Loads datasets from the "CS" Folder from "Data".
• Data Processing: Generates PSTH data, confidence intervals, and standard deviations, along with raw data processing.
• Visualization: Creates bar charts, heatmaps, and PSTH graphs using matplotlib.
• Results: Processed data and visualizations are saved in the corresponding data and figs directories.

2. Knob-doric-psth.ipynb

• Data Loading: Loads datasets from the "Knob" Folder from "Data".
• Data Processing: Generates PSTH data and associated statistics.
• Visualization: Creates various visualizations including bar charts, heatmaps, and PSTH graphs.
• Results: Processed data and visualizations are saved in the corresponding data and figs directories.

3. Stim-doric-psth.ipynb

• Data Loading: Loads datasets from the "Stim" Folder from "Data".
• Data Processing: Generates statistical analyses, including PSTH data and related statistics.
• Visualization: Creates visualizations such as bar charts, heatmaps, and PSTH graphs.
• Results: Processed data and visualizations are saved in the corresponding data and figs directories.

Python Files Overview

1. fileselector.py:

   • Purpose: Facilitates file selection and data loading for analysis tasks.
   • Features: Integrates with ipywidgets to create interactive UI elements for selecting files and loads datasets using pandas.

2. photometry_functions.py:

   • Purpose: Provides utility functions for processing and analyzing fiber photometry data.
   • Features: Functions to compute standardized dF/F signals and integrates with numpy and pandas for data manipulations.

3. dataexplorer.py:

   • Purpose: Designed to explore and process data from HDF5 files used in fiber photometry.
   • Features: Uses h5py to handle HDF5 files and integrates with numpy and pandas for data manipulations.

---

Is there anything specific you'd like to modify or add? Let me know if you'd like more details on any part of the documentation.

Project Structure

├── Data
│   ├── CS
│   │   ├── CS_file
│   │   │   ├── Data
│   │   │   │   └── *.csv
│   │   │   └── Figs
│   │   │       └── *.png
│   │   └── *.doric
│   ├── Knob
│   │   ├── Knob_file
│   │   │   ├── Data
│   │   │   │   └── *.csv
│   │   │   └── Figs
│   │   │       └── *.png
│   │   └── *.doric
│   └── stim
│   │   ├── Knob_file
│   │   │   ├── Data
│   │   │   │   └── *.csv
│   │   │   └── Figs
│   │   │       └── *.png
│   │   └── *.doric
├── Docs
├── .gitignore
├── CS-doric-psth.ipynb
├── Knob-doric-psth.ipynb
├── Stim-doric-psth.ipynb
├── dataexplorer.py
├── fileselector.py
└── photometry_functions.py

Contribution

For contributions, please reach out to the project maintainers through the repository's issue tracker or directly.