Installation

CytoBridge is currently under active development. You can install it using the methods outlined below:

Recommended Approach: Install via pip

Install CytoBridge quickly and easily using pip:

pip install CytoBridge

Developer Approach: Clone the Repository

This approach is suitable for developers who want to modify the source code or contribute to the project:

1. Clone the repository to your local machine

git clone https://github.com/zhenyiizhang/CytoBridge.git

2. Set up a Conda environment to manage dependencies
   Follow the steps below to create an isolated environment for CytoBridge:

   (1) Create and activate a new Conda environment

   conda create -n CytoBridge python=3.10 ipykernel -y
   conda activate CytoBridge
   

   (2) Navigate to the root directory of the cloned repository

   cd path_to_CytoBridge
   

   (3) Install all required dependencies

   pip install -r requirements.txt
   

Update Log

CytoBridge 1.2 (2025-10-29)

• score component released → stochastic dynamics ready

• RUOT pipeline stable under default hyper-params (config/ruot)

• New plots: velocity/score/V+S streams, 2-D score (density) and ODE/SDE trajectories.

• evuluation and test.ipynb refreshed with downstream examples

CytoBridge 1.3 (2025-11-25)

• interaction component released → cell-cell communication. ready

• Conditional Flow Matching and CytoBrigde (interaction) pipeline stable under default hyper-params (config/ruot)

• New plots: interaction_stream, interaction_potential, landscape , process_sde_classification and analyze_terminal_states

• test refreshed with downstream examples

CytoBridge 1.4 (2025-12-01)

• Debug and Optimization: Improved preprocessing to better adapt to real-world datasets.

• Documentation Enhancements: Refined the installation and guide to provide clearer instructions and better user guidance.