Getting Started

This page is the shortest path from zero setup to first successful ingest + first analysis query.

1. Clone repositories side-by-side

ADAMACS is used as two repos:

  • adamacs_ingest (ingest/task staging) - CLONE

  • adamacs_analysis (querying/analysis notebooks) - FORK

cd /path/to/workspace
git clone https://github.com/SFB1089/adamacs_ingest.git
git clone https://github.com/YOUR-FORK/adamacs_analysis.git

or (likely) when using ssh access:

cd /path/to/workspace
git clone git@github.com:SFB1089/adamacs_ingest.git
git clone git@github.com:YOUR-FORK/adamacs_analysis.git

2. Install environment

Recommended:

cd /path/to/workspace/adamacs_analysis
./scripts/install_datajoint_analysis.sh

For detailed install options, use Common -> Environment Setup.

3. Create local DataJoint config

Create local config files:

cd /path/to/workspace/adamacs_ingest
cp Example_dj_local_conf.json dj_local_conf.json

cd /path/to/workspace/adamacs_analysis
cp Example_dj_local_conf.json dj_local_conf.json

Then set host/user/password/path values for your account. Reference: Common -> dj_local_conf.

4. Verify DB connection

In your configured environment:

import datajoint as dj
dj.conn()
print("Connected")

If this fails: Common -> Troubleshooting.

5. Do first ingest + first analysis check

First ingest:

from adamacs.gui import select_sessions
select_sessions(["XX_ANM-0000_2026-01-01_sessXXXX_scanXXXX"])

Then open analysis notebook:

  • adamacs_analysis/notebooks/01_querying_guide.ipynb

Workflow rules

  • Stage ingest/task rows from GUI.

  • Let workers run heavy populations.

  • Analyze in adamacs_analysis.