CalciumZero: A user-friendly prep processing pipeline for fluorescence calcium imaging

• Features
• Run

Running the pipeline:

• You can use our pre-built GUI application. Download based on your platform here.
• If you encounter problems for our GUI application, please submit an issue.
• You can directly run it on Google Colab. See Colab Instructions to run it within Colab.
• You can run it using our Docker image.
• [Discouraged] You can manually install all the dependencies to manually run it and further develop on it. See Instructions on local for a detailed explanation.

Configure environment

If you just want to interact and use this work, the best way is to launch our provided application package across platorm.

OS	Windows	MacOS	Ubuntu
Installer	link	link	link
If you want to develop this application further, you can refer to Instructions on local to run it locally.

Running on Colab

You will need to follow the link here to our Colab notebook. Note that our Colab notebook is lightweight, free to go. Prior to run the pipeline on Colab, you should have your input files located in your Google Drive. At the beginning of the notebook, we will ask you for permissions to mount your Google Drive on Google Colab runtime.

Running on Docker

Docker Image is already on DockerHub. Current version: 0.1.

• First make sure you have Docker installed on your computer.
• Pull the docker image using command docker image pull canying0913/caiman_pipeline:0.1.
• Download our provided launch script. Use python to run this script, as it will launch a container with the image we just pulled. If you need help with using the launcher script, you can run python3 run_pipeline.py -h to have a detailed explanation on its parameters.