DriftlessMap

Interactive histology registration and brain-atlas mapping.

DriftlessMap is an open-source desktop application for registering histological images to reference brain atlases, reconstructing probes and other anatomical objects, and visualizing data in 2D and 3D. The name refers to Wisconsin's Driftless Area and to the project's focus on dependable spatial mapping.

Origin and independence

DriftlessMap began as a fork of HERBS — Histological E-data Registration in rodent Brain Spaces — originally created by Jingyi Guo Fuglstad, Pearl Saldanha, Jacopo Paglia, Jonathan R. Whitlock, and HERBS contributors.

DriftlessMap is independently maintained. It is not affiliated with or endorsed by the original HERBS developers. Their foundational work remains credited in the Git history, license, project history, contributors, authors, and acknowledgements.

Current development is led by Mohebi & Associates, with Ali Mohebi as project lead and maintainer.

If DriftlessMap contributes to published research, please cite both the software version used and the original HERBS paper:

Fuglstad, J. G., Saldanha, P., Paglia, J., & Whitlock, J. R. (2023). Histological E-data Registration in rodent Brain Spaces. eLife, 12, e83496. https://doi.org/10.7554/eLife.83496

See CITATION.cff for machine-readable citation metadata.

Features

• 2D and 3D visualization of volumetric brain atlases and arbitrary slices.
• Interactive histology-to-atlas registration with local elastic deformation.
• Automatic suggestions for the matching atlas section and starting landmarks.
• Probe planning, reconstruction, contact mapping, and CSV export.
• Drawing, cell, virus-expression, and user-defined object workflows.
• Safe, versioned project and object archives.
• Support for custom compatible atlases.

Installation

DriftlessMap 1.6.1 is available as a desktop application for end users and as a Python package for developers.

Mode 1: desktop application for end users

No Python or Conda installation is required. Download the asset for your computer from GitHub Releases:

• Windows 64-bit: download DriftlessMap-1.6.1-Windows-x64.zip, extract the complete folder, and double-click DriftlessMap.exe. Do not move the executable out of its extracted folder.
• macOS (Apple Silicon): download DriftlessMap-1.6.1-macOS-arm64.dmg, open it, and drag DriftlessMap.app to Applications. The application bundle includes the DriftlessMap icon and all Python dependencies. Intel Macs are not covered by the desktop build; use the Conda/pip installation below.

Release builds are currently unsigned. If Windows SmartScreen or macOS Gatekeeper displays a warning, verify that the file came from the official release page before bypassing the warning. Code signing and notarization are planned for a future release.

If macOS reports that Apple could not verify that DriftlessMap is free of malware:

1. Click Done; do not move the application to the Trash.
2. Drag DriftlessMap.app from the DMG into Applications.
3. In Finder, Control-click DriftlessMap.app, choose Open, and confirm Open if macOS offers that option.
4. If the same warning remains, open System Settings, select Privacy & Security, scroll to Security, and click Open Anyway beside the DriftlessMap message.
5. Authenticate when prompted and confirm Open. This approval is normally required only for the first launch.

Only use Open Anyway for a copy downloaded from the official DriftlessMap 1.6.1 release. The official macOS DMG has this SHA-256 digest:

aa8ed43826e63cd1e111e3ee53310bb1ac569fd1409862070b847afaeefe7e94

Mode 2: Conda and pip for developers

DriftlessMap supports Python 3.10–3.14 and Qt 6 through PyQt6. Python 3.14 is recommended for core development:

conda create --name DriftlessMap python=3.14 -y
conda activate DriftlessMap
python -m pip install --upgrade pip
git clone https://github.com/mohebi-n-associates/DriftlessMap.git
cd DriftlessMap
python -m pip install -e ".[test]"

Launch the editable installation with driftlessmap or python -m driftlessmap. Library users can call driftlessmap.run().

To use the stable PyPI package instead of an editable checkout, run:

python -m pip install driftlessmap

Check your version and upgrade

Check the installed version:

python -m driftlessmap --version

Compare it against the latest stable release on PyPI:

pip index versions driftlessmap

Upgrade to the latest stable release:

python -m pip install --upgrade driftlessmap

Zeiss CZI files

CZI support uses the optional aicspylibczi package, whose prebuilt packages currently support Python through 3.13:

conda create --name DriftlessMap-CZI python=3.13 -y
conda activate DriftlessMap-CZI
python -m pip install --upgrade pip
python -m pip install "driftlessmap[czi]"

Building the desktop applications

Native applications must be built on their target operating system. The release workflow builds both platforms automatically; maintainers can also run packaging/build_windows.ps1 on Windows or packaging/build_macos.sh on macOS. Outputs are written to dist/ as a Windows ZIP and a macOS DMG.

Compatibility with HERBS

The rebrand is designed not to strand existing research data:

• DriftlessMap reads legacy .herbs, .herbslayer, .herbsobj, .herbsslice, and .herbstri files.
• New files use .dmap, .dmaplayer, .dmapobj, .dmapslice, and .dmaptri.
• DriftlessMap installs only the driftlessmap Python package and command. It does not overwrite the original HERBS package, so both distributions can be installed in the same environment. New code should use import driftlessmap.
• Existing HERBS_CONFIG_DIR overrides remain supported. New configurations should use DRIFTLESSMAP_CONFIG_DIR.
• Some persisted coordinate field names retain herbs because changing them would break existing datasets and downstream analysis scripts.

The original HERBS application may not be able to open files newly written by DriftlessMap. Keep backups before converting important projects.

Documentation

Read the DriftlessMap User Manual for installation, atlas, registration, reconstruction, persistence, export, and troubleshooting guidance. The original HERBS Cookbook and tutorials remain useful for workflows whose interface has not changed.

The screenshot below is retained from HERBS for historical workflow reference; its title bar predates the DriftlessMap rebrand.

Do not store downloaded atlases inside the source or installed package directory. Keep each atlas in its own external folder.

See What’s New in DriftlessMap for release history and migration notes.

License

DriftlessMap is distributed under the MIT License. The original HERBS copyright and permission notice are preserved, and a separate copyright notice covers subsequent DriftlessMap modifications. See LICENSE.txt and ORIGINS.md.

Please report issues or start discussions at https://github.com/mohebi-n-associates/DriftlessMap.