Processing Multibeam Data | Caroline Williams

Global Multi-Resolution Topography (GMRT) bathymetric map showing ocean floor detail worldwide — Global Multi-Resolution Topography (GMRT) synthesis — the continuously updated global bathymetric model that this workflow contributes to. Data: GMRT/LDEO, CC BY 4.0.

This training manual was developed during my practicum at Columbia University's Lamont-Doherty Earth Observatory under the mentorship of Vicki Ferrini. It documents the complete GMRT (Global Multi-Resolution Topography) quality assessment and quality control workflow for processing multibeam bathymetric data used in global seafloor mapping.

The manual covers every step from logging into the server, editing multibeam sonar data in MBedit, verifying edits in GeoMapApp, through to the full processing pipeline that integrates corrected data into GMRT's global bathymetric model.

1. Overview & Purpose

GMRT (Global Multi-Resolution Topography) integrates bathymetric measurements into global seafloor grids, which are used for scientific research, policy decisions, and oceanographic exploration.

As an editor, your role is to clean, verify, and edit multibeam sonar data using MBedit, and then confirm edits by reviewing the Preview Tiles using GeoMapApp. These contributions ensure that GMRT maintains high-quality, production-ready bathymetric datasets.

Why This Matters

Understanding the full workflow — from logging in, editing data, to running Reproc — gives context to your edits and ensures accuracy. Your work directly contributes to a global resource used by researchers worldwide.

2. System Requirements & Environment

VPN Access

You must connect to Lamont-Doherty's internal network. A VPN secures the connection, allowing access to GMRT servers, cruise folders, and authentication systems. Without VPN, MBedit and GeoMapApp cannot connect to the content you are working on.

Operating System

Mac/Linux: MBedit and GMRT tools can be run through the Terminal application; minimal configuration needed.

Windows: Requires VirtualBox with a preconfigured Linux virtual machine (GMRT_Benthos) for access.

3. Logging into the GMRT Server

1
Start Virtual Machine (Windows users)
Open VirtualBox, select GMRT_Benthos, and click START.
2
Open Terminal
In the VM, open LX Terminal from the bottom taskbar.
3
SSH Login
Type the SSH command below, enter your password when prompted.

ssh -X -Y -C yourusername@gmrt-ldeo.ldeo.columbia.edu

SSH Flags Explained

-X Enables X11 forwarding (required for graphical tools)

-Y Trusted X11 forwarding (MBedit interface depends on this)

-C Compression for faster data transfer over VPN

4. Navigating the GMRT Filesystem

1
Enter the GMRT environment
Type gmrt and press Enter
2
List cruise directories
Type ls and press Enter
3
Navigate to your cruise
Type cd Thompson/TN364 and press Enter
4
Open the first data file in MBedit

mbedit -f -1 -i TN364.gmrt.mb-1

Important

Always verify you are in the correct cruise directory before editing. Editing files in the wrong directory could overwrite other users' work.

5. Editing Multibeam Data in MBedit

MBedit is the primary tool for cleaning and validating multibeam data. It allows you to remove noise, spikes, and artifacts to prepare high-quality bathymetric datasets.

Set Preferences

1
Open View → Click Along Track View
2
Open File → Click File Selection List
Select <eaf> → Edit Selected File
3
When prompted "Apply saved edits to the data?"
Click Yes

Vertical Exaggeration

Set between 6–8 to enhance subtle seafloor features. This helps detect noise, beam jumps, or errors that might otherwise be invisible.

Pings Shown vs. Pings to Step

Pings Shown: Number of profiles displayed on screen.
Pings to Step: Number of pings advanced when moving forward.
Keep Pings Shown > Pings to Step for better editing context.

GMRT bathymetry of the Mid-Atlantic Ridge showing multibeam swath data detail — Mid-Atlantic Ridge bathymetry from GMRT — this level of seafloor detail is achieved through the multibeam editing process described above. The ridge's central rift valley and transform faults are clearly visible in the processed data.

6. Viewing Edits in GeoMapApp

GeoMapApp allows QA/QC of your edited tiles. You can examine your edits against the production version of GMRT and verify coverage and metadata.

1
Open GeoMapApp → File → Preferences → Select GMRT Tiles
2
Load Cruise Tiles from Server → Select Todo → Select cruise → Production → Yes
3
Zoom using telescope icon → set Zoom = 512
4
Navigate using hand tool to your edited section

Layer Manager

Shows all visible layers and their order. Toggle layers to isolate your cruise tiles.

Loaded Grids

Shows all loaded raster grids (Preview Tiles), their metadata, and resolution.

DEM (Digital Elevation Model)

Gridded seafloor depth representation used for visualization, analysis, and tile integration.

GMRT bathymetry of the Hawaiian Ridge showing volcanic island chain and seamounts — Hawaiian Ridge bathymetry from GMRT — GeoMapApp enables editors to verify their tile edits against the production dataset, checking for artifacts and ensuring seamless integration with adjacent survey data.

7. GMRT Processing Pipeline

Understanding the pipeline ensures clarity about when your edits are integrated into the global dataset.

Preproc

Preprocessing

Automated initial processing of raw multibeam data. Decodes sensor data, applies error checks, generates first-pass Preview Tiles. Editors don't run this directly.

Reproc

Reprocessing

Applies your manual edits to Preview Tiles. Run after editing to ensure corrections are integrated. Critical for publication-ready datasets.

Postproc

Post-Processing

Final step that prepares data for integration into GMRT production tiles and public access through MGDS. Fully automated after Reproc.

Running Reproc

# Navigate to cruise directory
gmrt
cd Thompson/TN364

# Run Reproc
GMRT_reproc -e TN364 > & reproc.log &

# Verify (press Enter a few times — no errors = success)

8. Quick Reference Checklist

Connect VPN

Open terminal

SSH to gmrt-ldeo.columbia.edu

Change directories to GMRT work directory

Navigate to cruise

Open MBedit → Set vertical exaggeration → Select Along Track View

Edit file → Forward → Next File

Open GeoMapApp → Load tiles → Zoom 512 → Check edits

Quit MBedit → Exit terminal → Power off VM

9. Glossary

Click each category to expand definitions.

10. Frequently Asked Questions

Collection Methods

What are the different ways seafloor data can be collected?

Multibeam Echo Sounders (MBES): Wide swaths with multiple beams
Single-Beam Echo Sounders (SBES): Depth directly below the ship
Side-Scan Sonar: Acoustic reflections for texture and features
AUVs and ROVs: High-resolution mapping in targeted areas
Satellite-Derived Bathymetry: Shallow water depth estimates from imagery
LIDAR: Airborne laser mapping in shallow waters or coastal areas

Data Loading & Processing

How is seafloor data loaded into a computer for editing?

Raw multibeam files are imported into processing software such as MB-System or GMRT. Preprocessing converts raw sonar, navigation, and attitude data into gridded tiles (cruise tiles). Editors then load these tiles into MBedit or GeoMapApp for quality control and manual corrections.

How is sonar data "cleaned" before being added to global maps?

Removing spikes, noise, and bad pings
Correcting for navigation errors and sound speed variations
Flagging problematic beams
Generating new production tiles via reprocessing pipelines

Visualization & Interpretation

What do the different colors on bathymetry maps represent?

Colors typically indicate depth: shallow areas in warm colors (reds, oranges) and deeper areas in cool colors (blues, purples). Color ramps help visualize terrain gradients, slope, and seafloor morphology.

Standards & Quality

How are data quality and accuracy verified?

Comparing preproc vs. reproc tiles
Checking for noise, spikes, or gaps in coverage
Confirming consistency with adjacent surveys and satellite-derived bathymetry
Cross-referencing with historical datasets or other institutional measurements