https://github.com/eulerlab/djimaging
2P imaging data joint tables and schemas
https://github.com/eulerlab/djimaging
Last synced: 11 months ago
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2P imaging data joint tables and schemas
- Host: GitHub
- URL: https://github.com/eulerlab/djimaging
- Owner: eulerlab
- License: mit
- Created: 2022-03-11T09:10:25.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2025-07-29T12:52:46.000Z (11 months ago)
- Last Synced: 2025-07-29T15:24:02.869Z (11 months ago)
- Language: Python
- Size: 900 KB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 15
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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:
```bash
git clone https://github.com/eulerlab/djimaging.git
````
Install the package e.g. using pip as an editable package:
```bash
cd djimaging
pip install -r requirements.txt
pip install -e .
```
If you want to use autorois, also install the following:
```
pip install -r requirements-autorois.txt
```
> ❗ 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
```bash
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!