U19 MATLAB Pipeline

This is a data pipeline, constructed in DataJoint, used across Princeton's U19. It specifies a number of tables and their relational structure to organizes all metadata to

• mouse management,
• training management,
• microscope management,
• und recording

in one coherent framework.

Installation

Prerequisite

• Install DataJoint for MATLAB
  • Utilize MATLAB built-in GUI i.e. Top Ribbon -> Add-Ons -> Get Add-Ons
  • Search, select, and install DataJoint

User installation

• First time:

  • Add this repository to MATLAB Path or cd to this repository folder.
  • dj_initial_conf(1)
  • Insert user and password for the DB

• Subsequent times:

  • Add this repository to MATLAB Path or cd to this repository folder.
  • connect_datajoint00

Tutorial

Follow the steps to go through the tutorial:

1. Get into the directory of the current tutorial tutorials/202103/

2. Choose your tutorial

   • Querying data (Strongly recommended)

     • go through session01_queries_fetches.mlx

   • Building analysis pipeline (Recommended only if you are going to create new databases or tables for analysis)

     • go through session02_build_pipeline.mlx

Accessing data files on your system

• There are several data files (behavior, imaging & electrophysiology) that are referenced in the database

• To access these files you should mount PNI file server volumes on your system.

• There are three main file servers across PNI where data is stored (braininit, Bezos & u19_dj)

  On windows systems

  • From Windows Explorer, select "Map Network Drive" and enter:
    \\cup.pni.princeton.edu\braininit\ (for braininit)
    \\cup.pni.princeton.edu\Bezos-center\ (for Bezos)
    \\cup.pni.princeton.edu\u19_dj\ (for u19_dj)
    
  • Authenticate with your NetID and PU password (NOT your PNI password, which may be different). When prompted for your username, enter PRINCETON\netid (note that PRINCETON can be upper or lower case) where netid is your PU NetID.

  On OS X systems

  • Select "Go->Connect to Server..." from Finder and enter:
    smb://cup.pni.princeton.edu/braininit/ (for braininit)
    smb://cup.pni.princeton.edu/Bezos-center/ (for Bezos)
    smb://cup.pni.princeton.edu/u19_dj/ (for u19_dj)
    
  • Authenticate with your NetID and PU password (NOT your PNI password, which may be different).

  On Linux systems

  • Follow extra steps depicted in this link: https://npcdocs.princeton.edu/index.php/Mounting_the_PNI_file_server_on_your_desktop

  Notable data

  Here are some shortcuts to common used data accross PNI

  Sue Ann's Towers Task

  • Imaging: /Bezos-center/RigData/scope/bay3/sakoay/{protocol_name}/imaging/{subject_nickname}/
  • Behavior: /braininit/RigData/scope/bay3/sakoay/{protocol_name}/data/{subject_nickname}/

  Lucas Pinto's Widefield

  • Imaging /braininit/RigData/VRwidefield/widefield/{subject_nickname}/{session_date}/
  • Behavior /braininit/RigData/VRwidefield/behavior/lucas/blocksReboot/data/{subject_nickname}/

  Lucas Pinto's Opto inactivacion experiments

  • Imaging /braininit/RigData/VRLaser/LaserGalvo1/{subject_nickname}/
  • Behavior /braininit/RigData/VRLaser/behav/lucas/blocksReboot/data/{subject_nickname}/

  Reading behavior files directly from Database

  1. Mount needed file server
  2. Connect to the Database
  3. Create a structure with subject_fullname and session_date from the session
     key.subject_fullname = 'koay_K65'
key.session_Date = '2018-02-05'
     
  4. Read file
     [status, data] = lab.utils.read_behavior_file(key)

  Get path info for the session behavioral file

  1. Mount needed file server
  2. Connect to the Database
  3. Create a structure with subject_fullname and session_date from the session
     key.subject_fullname = 'koay_K65'
key.session_Date = '2018-02-05'
     
  4. Fetch filepath info: data_dir = fetch(acquisition.SessionStarted & key, 'remote_path_behavior_file');
[~, filepath] = lab.utils.get_path_from_official_dir(data_dir.remote_path_behavior_file);

Backend

The backend is a SQL server [MariaDB].

Integration into rigs.

The rigs talk to the database directly [SSL, wired connection].