ethierlab/doric_fiberphotometry

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.

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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.

doric_fiberphotometry's Issues

heatmap for wireless data

@siamakhaz heatmap doesn't work with wireless data structure and needs to be edited

AUC bar

@siamakhaz
I need to define a time period for the calculation of AUC values instead of before and after zero.

artifact removal

@siamakhaz I need artifact removal for wireless data to detect peak artifacts and interpolate the removed part

doric files cant be opned

it seems that the Doric changed their Doric file structure again so our code is not running and returns error in opening the file

PSTH for init

@siamakhaz I need two different PSTH graph:
Both with success and failure in the same graph but in one of them time zero is the time of init (we already have it in the current version)
and the other graph with time zero is equal to the time of occurrence of success/fail.

Openning wireless data

@siamakhaz wireless data has a different file structure and recorded with a 10k sample rate and cannot be opened