DriftlessMap 1.4.0

DriftlessMap 1.4.0 adds reproducible project persistence and native desktop distribution.

Highlights:

• Save Project now preserves registration/warping, atlas slice and tilt, embedded active histology raster, layers, objects, complete probe planning and reconstruction state, tool state, and layout.
• Source histology and processed atlases use checksummed provenance with relocation and verification. Portable projects can additionally stream the original histology source; processed volume atlases remain external to keep projects manageable.
• Standalone object and probe files support sharing and reuse without being required for project restoration.
• Native Windows x64 and macOS desktop applications include the DriftlessMap icon and display version 1.4.0 in the GUI.
• The README documents end-user desktop installation separately from the Conda/pip developer workflow.

See WhatsNew.md and MANUAL.md for complete details.

DriftlessMap 1.2.0

DriftlessMap 1.2.0

DriftlessMap 1.2.0 introduces a versioned probe-localization export designed for downstream electrophysiology and NWB workflows.

Highlights

• Adds labeled sampling along the complete reconstructed probe centerline.
• Assigns Allen CCF coordinates and anatomical structures to each track sample.
• Introduces probe-reconstruction export schema version 2.
• Records atlas, software, coordinate-system, and probe-geometry provenance.
• Enables downstream assignment of estimated unit depths to atlas coordinates and brain regions.

Four-file localization export

The Export probe localization files action now creates four companion CSV files:

• *_contacts.csv — physical probe contacts, ordered deepest to shallowest, with atlas coordinates and anatomical assignments.
• *_track.csv — labeled samples along the fitted probe centerline, ordered from insertion to tip and spaced no farther apart than one atlas voxel.
• *_trajectory.csv — insertion and tip coordinates, trajectory angles, fit-quality metrics, atlas metadata, schema version, DriftlessMap version, and probe tip-to-contact offset.
• *_regions.csv — anatomical-region summaries, including structure IDs, acronyms, names, contact counts, and reconstructed path lengths.

The new track table is the recommended input for assigning continuously estimated electrode or unit depths to anatomy.

Coordinate information

For recognized Allen Mouse CCFv3 atlases, exports include:

• Allen CCF voxel coordinates
• Physical atlas coordinates
• Allen structure ID, acronym, and name
• Distance from probe insertion
• Distance from the geometric probe tip

Estimated Bregma-relative values remain clearly identified as estimates and should not be interpreted as a formal Paxinos atlas registration.

Upgrade notes

Existing probes should be unmerged and re-merged in DriftlessMap 1.2.0 before export. This regenerates the reconstruction using schema version 2 and adds the complete labeled centerline.

Downstream applications should:

• Require reconstruction schema version 2 when unit-level localization is needed.
• Use *_track.csv for interpolation and region assignment.
• Use the tip-to-contact offset recorded in *_trajectory.csv.
• Preserve the exported atlas and software provenance.

The previous contact, trajectory, and region files remain available, but the new track file is required for reliable localization of arbitrary depths along the probe.

Validation

This release includes expanded tests covering:

• Centerline sampling and ordering
• Atlas-region assignment
• Four-file CSV generation
• Schema and software provenance
• Probe tip-to-contact metadata
• Package version and release metadata

DriftlessMap 1.1.0

DriftlessMap 1.1.0

This is the first release under the DriftlessMap name—an independently maintained continuation of HERBS for histology registration and brain-atlas mapping.

Highlights

• Renamed the application and Python distribution to DriftlessMap.
• Added the driftlessmap command, python -m driftlessmap, and import driftlessmap API.
• Moved the complete implementation into the driftlessmap Python namespace.
• Removed the legacy herbs package and command from this distribution, allowing DriftlessMap and original HERBS to coexist in the same Python environment.
• Added support for Python 3.10–3.14 and migrated the interface to PyQt6.
• Improved probe reconstruction, contact mapping, anatomical-region reporting, and CSV exports.
• Added safer, versioned project and object archives.
• Added stricter validation for atlas files, images, layers, coordinates, meshes, and downloaded resources.
• Added automated testing across supported Python versions and secure PyPI publishing.

File compatibility

DriftlessMap continues to read legacy HERBS files:

• .herbs
• .herbslayer
• .herbsobj
• .herbsslice
• .herbstri

Newly saved files use the DriftlessMap formats:

• .dmap
• .dmaplayer
• .dmapobj
• .dmapslice
• .dmaptri

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

Installation

Create a dedicated environment and install from PyPI:

conda create --name DriftlessMap python=3.14 -y
conda activate DriftlessMap
python -m pip install --upgrade pip
python -m pip install driftlessmap
driftlessmap

For optional Zeiss CZI support, use Python 3.13:

python -m pip install "driftlessmap[czi]"

Attribution

DriftlessMap began as a fork of HERBS and preserves the original project’s copyright notice, MIT License, Git history, authorship, and publication credit.

Original HERBS publication:

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

Current development and maintenance are led by:

• Mohebi & Associates
• Ali Mohebi

DriftlessMap is independently maintained and is not affiliated with or endorsed by the original HERBS developers.

See the full release history and project origins for additional details.