OCNC_tutorial_optinist

This repository provides instructions for the preparation for the Optinist tutorial at OCNC2024. Please download the Docker image for the Optinist tutorial and make sure it opens correctly.

In addition, please download sample files from this link

preparation

1. start the Docker Desktop application.
   (For M1/2 Mac users, make sure 'Rosetta for x86_64/amd64 emulation on Apple Silicon' is checked in the settings for Docker Desktop. )

3. Open a Terminal/Command prompt/PowerShell and execute the following to fetch the Docker image.

docker pull oistncu/optinist-allinone

3. Create and run the container by the following command.

docker run -it --shm-size=2G -v YOURSAVINGDIRECTORY:/app/studio_data --env OPTINIST_DIR="/app/studio_data" --name optinist_container -d -p 8000:8000 --restart=unless-stopped oistncu/optinist-allinone:latest poetry run python main.py --host 0.0.0.0 --port 8000

• The -v option in docker run mounts a path from the host to a path in the container. Substitute YOURSAVINGDIRECTORY to your own path. For example, C:/tmp(in Windows) or /tmp (in Mac) will assign the temporary directory of the host.

• The container automatically starts optinist. When the initialization is finished, they show the logs like this.

4. After you see the logs, open a web browser (Google Chrome is recommended) and go to http://localhost:8000.

• If you see this, you have successfully launched the application.

trouble shooting

Issue: The Docker container seems to be working, but http://localhost:8000 does not show the front page of OptiNiSt.
Solution: Try using 127.0.0.1 instead of localhost.

other information mentioned in the tutorial

OptiNiSt

• documentation
• gitub repository

NWB

• project
• NWB software
• HDF view

cell detection algorithms

  suite2p  website github repository   paper
  CaImAn  website  github repository paper
  lccd  gitub repository  paper