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Setup database access

To have full access to the Buzsaki lab databank with CellExplorer, there are two necessary steps you have to do in Matlab: add your credentials and define the repository paths. Public reference data can still be used without credentials.

This page is mostly dedicated to lab members. There is no need to setup db access if you do not already have an account.

1. Add your db credentials

Once CellExplorer has been added to your Matlab Set Path, you should provide your credentials in the file db_credentials.m. In the Matlab Command Window type:

edit db_credentials.m

In the credentials file, replace the two lines below with your credentials:

credentials.username = 'user';
credentials.password = 'password';

2. Define paths to data repositories

Paths are generated from the repository definition in the database. Here you need to define the root path for each repository in db_local_repositories.m. To use the NYUshare_Datasets (the NYU share dataset directory), you must define the system path to the repository, e.g.:

repositories.NYUshare_Datasets = '/Volumes/buzsakilab/Buzsakilabspace/Datasets';

Likewise to link to data located in NYUshare_Peter, provide the system path to the repository:

repositories.NYUshare_Peter = '/Volumes/buzsakilab/peterp03/IntanData';

This system allows you to define paths that are specific to each computer-system and separates system-access from the data storage solution, which could be a local drive hard drive, a centralized network storage, or another storage solutions.

3. Test db connection

Now you can test the connection by typing:

sessionTest = 'Peter_MS10_170307_154746_concat';
sessions = db_load_sessions('sessionName',sessionTest);
session = sessions{1};

If succesfull it will create the session struct in your workspace containing metadata for that session. You can learn more about the data structure and format here.

There are a couple of database example calls in the Matlab script db_example.m located in the db folder.