CIVIS

CIVIS is a Calcium Imaging data visualization server built with Bokeh and Flask. It provides an interactive web-based interface for visualizing and analyzing calcium imaging data, facilitating research and data exploration.

Table of Contents

• Features
• Installation
• Setup
• Running the Server

Features

• Interactive Visualizations: Utilize Bokeh for dynamic and responsive data visualizations.
• Web Interface: Powered by Flask, offering an accessible web interface for data interaction.
• Modular Architecture: Supports multiple visualization modules such as labelers, trajectories, connections, rasters, and place finders.
• Customizable Configuration: Easily configure data paths and server settings through a JSON file.
• Scalable Server: Capable of handling multiple Bokeh applications concurrently.

Installation

Prerequisites

• Python: Version 3.9 or higher
• pip: Python package installer

Clone the Repository

git clone https://github.com/boyuan99/civis.git
cd civis

Create a Conda Environment

conda env create -f environment.yaml
conda activate civis

Note: The environment.yaml file includes the command to install your package in editable mode (pip install -e .). This means that after activating the environment, your package is already set up for development.

Setup

1. Configuration File:

   Use the provided civis/config.example.json as a template to create your local config.json. This file includes paths to necessary data directories.

   cp civis/config.example.json civis/config.json

2. Edit Configuration:

   Open civis/config.json and update the paths to match your local data directories:

   {
     "ProcessedFilePath": "path/to/ProcessedData/",
     "VirmenFilePath": "path/to/VirmenData/",
     "LabelsPath": "path/to/ProcessedData/",
     "ElecPath": "path/to/ElecData/"
   }

   Note: Ensure all paths are absolute or relative to the project root and that they point to valid directories containing your data.

Running the Server

Default Ports

By default, running the server will open two ports:

• Flask Server: 8000
• Bokeh Server: 5006

Start the Server

Execute the following command to start the civis:

civis

Custom Ports

To specify custom ports for the Flask and Bokeh servers, use the --flask-port and --bokeh-port flags:

civis --flask-port 8000 --bokeh-port 5006

Accessing the Application

Once the server is running, open your web browser and navigate to:

http://localhost:8000

You will see the home page, from which you can access various visualization modules such as Labeler, Trajectory, Connection, Raster, and Place applications.