A User-Friendly Program for Evaluating Cell-Cell Binding

This software package was generated in association with the following manuscript, which is currently available as a pre-print:

CELLISA – a cell-cell binding assay for evaluation of nanovesicle targeting proteins

Taylor F. Gunnels, Jonathan D. Boucher, Yazeed S. Alroogi, Neha P. Kamat, Joshua N. Leonard

bioRxiv : pending

This package was developed to accompany an experimental workflow for quantifying cell membrane-displayed protein interactions with target proteins on other cell membranes. The approach quantifies cell-cell interactions between two “bait” and “prey” cells which are each labeled with distinct fluorescent markers. The software package quantifies such interactions by evaluating matched sets of fluorescent micrograph images, as described in detail in the manuscript.

For an in-depth description of how to install and use the CELLISA package, please see the CELLISA User Guide

• Python
• A Python Interpreter
• Miniconda

For more information on how to access these prerequisites, please see the CELLISA User Guide.

The CELLISA package uses a few dependencies to run, and it automatically downloads them to your environment. However, we highly recommend using a separate conda environment for CELLISA as it makes things more organized and smooth. You can use the dedicated CELLISA environment (included in the package files) to do this.

Included in the package folder is an environment file that you can use to copy the CELLISA conda environment using the following steps:

1. Download and install Miniconda (if you already have it on your computer, please skip this step)

   a. Download the Miniconda installer from https://www.anaconda.com/download

b. Open the downloaded Miniconda .exe file and follow the steps for installation

2. Launch VSCode and open the CELLISA package folder
3. Navigate to the dedicated VSCode terminal at the bottom of the screen. If it is not open press ctrl+`

4. In the CELLISA package folder, click on the environment file and copy its path

   

5. Back on the VSCode terminal copy the following command to create the virtual environment and replace "env_path" with the environment file path you copied in Step 4:

conda env create -n cellisa_env -f env_path

6. Once the environment is installed, close all VSCode windows and reopen the CELLISA main program. In the terminal activate the CELLISA conda environment using the following command:

conda activate cellisa_env

7. Finally, to use this environment navigate to the top right of the VSCode window and select the cellisa_env as the the kernel

8. Click "Select Another Kernel..." --> "Python Environments" --> "cellisa_env"

Now you can run the program with all required dependencies without further installations.