djimaging

2P imaging data joint tables and schemas

Getting started

Create a MySQL account

Ask IT to create a MySQL user account for you. They will send you a username and activation password.

❗ You probably don't want your own local MySQL server, so don't try to set one up but get access to the shared one.

Create a remote docker container

Create a docker container and install this package and its requirements in it.

Download the package:

git clone https://github.com/eulerlab/djimaging.git

Install the package e.g. using pip as an editable package:

cd djimaging
pip install -r requirements.txt
pip install -e .

❗ To test if the package was successfully installed, e.g. open a jupyter notebook in your container and call import djimaging.

Create a config file

Create a datajoint config *.json file, e.g. based on the template djimaging/djconfig/djconf_template.json. Fill out the missing values; if you don't know how, ask someone in your group.

❗ Never upload this personal config file to GitHub.

Create a user folder

Inside the root folder djimaging (not in djimaging/djimaging) run the make user script my calling

python3 make_user.py your_username_here

This will create a folder djimaging/djimaging/user/your_username_here/notebooks with some tutorial notebooks.

❗ Per default everything in this folder will not be under version control. Consider adding an expectation for your files here, but do not upload them to the shared repository. Do not upload personal config files.

Clean up

When you no longer need your test schema, make sure you drop it by calling schema.drop() and confirm by entering yes.

⚠️ Make sure you only drop your own schema! schema.drop() will show you the name of the schema. If you are not sure about the schema's origin, don't drop it!