driftlessmap 1.1.0__tar.gz

driftlessmap-1.1.0/AUTHOR.txt

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+DriftlessMap maintenance and development:
+- Mohebi & Associates: https://www.mohebi-associates.org/
+- Ali Mohebi: https://www.mohebial.com/
+
+Original HERBS authors:
+- Jingyi Guo Fuglstad
+- Pearl Saldanha
+- Jacopo Paglia
+- Jonathan R. Whitlock
+
+Original HERBS design, development, and CookBook: Jingyi Guo Fuglstad
+
+DriftlessMap is an independent continuation of HERBS. See ORIGINS.md for the
+complete project lineage, original publication, and contributor credits.
+
+
+Institutions
+------------

driftlessmap-1.1.0/CITATION.cff

@@ -0,0 +1,35 @@
+cff-version: 1.2.0
+message: >-
+  If you use DriftlessMap, cite the software version you used and the original
+  HERBS paper listed under references.
+title: DriftlessMap
+type: software
+version: 1.1.0
+authors:
+  - name: Mohebi & Associates
+    website: https://www.mohebi-associates.org/
+  - family-names: Mohebi
+    given-names: Ali
+    website: https://www.mohebial.com/
+repository-code: https://github.com/mohebi-n-associates/DriftlessMap
+url: https://github.com/mohebi-n-associates/DriftlessMap
+license: MIT
+abstract: >-
+  An interactive desktop application for histological image registration,
+  brain-atlas mapping, probe reconstruction, and anatomical data visualization.
+references:
+  - type: article
+    title: Histological E-data Registration in rodent Brain Spaces
+    authors:
+      - family-names: Fuglstad
+        given-names: Jingyi Guo
+      - family-names: Saldanha
+        given-names: Pearl
+      - family-names: Paglia
+        given-names: Jacopo
+      - family-names: Whitlock
+        given-names: Jonathan R.
+    journal: eLife
+    volume: 12
+    year: 2023
+    doi: 10.7554/eLife.83496

driftlessmap-1.1.0/CONTRIBUTORS.md

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+# Contributors
+
+## DriftlessMap
+
+DriftlessMap is maintained and developed by:
+
+- [Mohebi & Associates](https://www.mohebi-associates.org/)
+- [Ali Mohebi](https://www.mohebial.com/) — project lead and maintainer
+- Additional contributors recorded in the repository's Git history
+
+## Original HERBS project
+
+DriftlessMap began as a fork of HERBS. The original authors are:
+
+- Jingyi Guo Fuglstad
+- Pearl Saldanha
+- Jacopo Paglia
+- Jonathan R. Whitlock
+- Additional HERBS contributors recorded in the inherited Git history and
+  `THANKS.txt`
+
+The original project, publication, license, and complete relationship to
+DriftlessMap are documented in [ORIGINS.md](ORIGINS.md).

driftlessmap-1.1.0/LICENSE.txt

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+MIT License
+
+Copyright (c) 2022 HERBS Developers.
+All rights reserved.
+Copyright (c) 2026 Ali Mohebi and DriftlessMap contributors.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

driftlessmap-1.1.0/MANIFEST.in

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+#
+# Use .add_data_files and .add_data_dir methods in a appropriate
+# setup.py files to include non-python files such as documentation,
+# data, etc files to distribution (*for installation*).
+# Avoid using MANIFEST.in for that.
+#
+# Files in top-level directory:
+include AUTHOR.txt
+include CITATION.cff
+include CONTRIBUTORS.md
+include LICENSE.txt
+include MANIFEST.in
+include ORIGINS.md
+include pyproject.toml
+include README.md
+include WhatsNew.md
+include setup.py
+include THANKS.txt 
+
+include driftlessmap/main_window.ui
+
+include driftlessmap/data/query.csv
+include driftlessmap/data/atlas_labels.pkl
+
+# Included are: icons/, data/, qss/
+recursive-include driftlessmap/icons *.svg
+recursive-include driftlessmap/icons *.png
+
+recursive-include driftlessmap/qss *.qss
+
+global-exclude .DS_Store

driftlessmap-1.1.0/ORIGINS.md

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+# Project origins and attribution
+
+## Relationship to HERBS
+
+DriftlessMap is an independent open-source continuation of HERBS (Histological
+E-data Registration in rodent Brain Spaces). It retains substantial portions of
+the original HERBS code and therefore remains a derivative work under the MIT
+License.
+
+- Original project: <https://github.com/Whitlock-Group/HERBS>
+- Original license: MIT
+- Recorded upstream base commit: `7a181097a57d9f34b189f233a484a0f0c228c5da`
+- Independent project: <https://github.com/mohebi-n-associates/DriftlessMap>
+
+DriftlessMap is not affiliated with or endorsed by the original HERBS
+developers or the Whitlock Group.
+
+## Original authors and publication
+
+The original HERBS research software and publication were created by:
+
+- Jingyi Guo Fuglstad
+- Pearl Saldanha
+- Jacopo Paglia
+- Jonathan R. Whitlock
+- Additional HERBS code, testing, documentation, and research contributors
+  recorded in the repository history and `THANKS.txt`
+
+Original publication:
+
+Fuglstad JG, Saldanha P, Paglia J, Whitlock JR. Histological E-data
+Registration in rodent Brain Spaces. *eLife*. 2023;12:e83496.
+<https://doi.org/10.7554/eLife.83496>
+
+The original software is also identified as RRID:SCR_022776.
+
+## Independent development
+
+Independent work after the upstream base includes platform modernization,
+current Python and Qt support, safer persistence, validation and security
+hardening, automated regression tests, atlas-coordinate corrections, probe
+reconstruction and CSV export, ROI analysis, and expanded documentation.
+The Git history is intentionally preserved so individual contributions remain
+auditable.
+
+DriftlessMap development is led by
+[Mohebi & Associates](https://www.mohebi-associates.org/) and
+[Ali Mohebi](https://www.mohebial.com/). See `CONTRIBUTORS.md` for the current
+and original contributor groups.
+
+## Licensing and notices
+
+The complete project remains licensed under the MIT License:
+
+- The original `Copyright (c) 2022 HERBS Developers` notice is preserved
+  verbatim in `LICENSE.txt`.
+- `Copyright (c) 2026 Ali Mohebi and DriftlessMap contributors` covers
+  subsequent modifications.
+- Neither the new project name nor this attribution statement changes the
+  license governing the original HERBS code.
+
+When redistributing DriftlessMap or a substantial portion of its source, retain
+`LICENSE.txt`. Preserving this file is a condition of the MIT License.
+
+## Compatibility names
+
+Names such as `.herbs*` legacy file extensions, `HERBS_CONFIG_DIR`, and
+persisted `herbs_vox` coordinate fields are retained only where needed for data
+compatibility. DriftlessMap does not install a top-level `herbs` Python package
+or a `herbs` command. These compatibility names do not indicate affiliation
+with or endorsement by the original HERBS developers.

driftlessmap-1.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: driftlessmap
+Version: 1.1.0
+Summary: Interactive histology registration and brain-atlas mapping
+Author: Pearl Saldanha, Jacopo Paglia, Jonathan R. Whitlock, Mohebi & Associates, Ali Mohebi
+Author-email: Jingyi Guo Fuglstad <jingyi.g.fuglstad@gmail.com>
+Maintainer: Mohebi & Associates, Ali Mohebi
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/mohebi-n-associates/DriftlessMap
+Project-URL: Bug Tracker, https://github.com/mohebi-n-associates/DriftlessMap/issues
+Project-URL: Documentation, https://github.com/mohebi-n-associates/DriftlessMap#readme
+Project-URL: Maintaining Organization, https://www.mohebi-associates.org/
+Project-URL: Lead Maintainer, https://www.mohebial.com/
+Keywords: brain atlas,histological image registration,probe coordinates
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Education
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: MacOS
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: PyQt6<7,>=6.8
+Requires-Dist: pyqtgraph<0.15,>=0.14
+Requires-Dist: PyOpenGL<4,>=3.1.7
+Requires-Dist: superqt<0.9,>=0.8
+Requires-Dist: opencv-python<6,>=4.10
+Requires-Dist: numba<1,>=0.61
+Requires-Dist: numpy<3,>=2.0
+Requires-Dist: scipy<2,>=1.13
+Requires-Dist: requests<3,>=2.32
+Requires-Dist: nibabel<6,>=5.2
+Requires-Dist: pynrrd<2,>=1.0
+Requires-Dist: tifffile>=2024.7
+Requires-Dist: pandas<4,>=2.2
+Requires-Dist: natsort<9,>=8.4
+Requires-Dist: imagecodecs>=2024.6
+Provides-Extra: czi
+Requires-Dist: aicspylibczi>=3.3.1; python_version < "3.14" and extra == "czi"
+Provides-Extra: test
+Requires-Dist: pytest>=8.3; extra == "test"
+Requires-Dist: ruff>=0.9; extra == "test"
+Requires-Dist: tomli>=2; python_version < "3.11" and extra == "test"
+Dynamic: license-file
+
+# 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](https://github.com/Whitlock-Group/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](LICENSE.txt), [project history](ORIGINS.md),
+[contributors](CONTRIBUTORS.md), [authors](AUTHOR.txt), and
+[acknowledgements](THANKS.txt).
+
+Current development is led by
+[Mohebi & Associates](https://www.mohebi-associates.org/), with
+[Ali Mohebi](https://www.mohebial.com/) 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](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.
+- 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.
+
+## Install
+
+DriftlessMap 1.1.0 supports Python 3.10–3.14 and Qt 6 through PyQt6. Python
+3.14 in a dedicated environment is recommended for new installations.
+
+```bash
+conda create --name DriftlessMap python=3.14 -y
+conda activate DriftlessMap
+python -m pip install --upgrade pip
+python -m pip install driftlessmap
+```
+
+Launch the application with any of:
+
+```bash
+driftlessmap
+python -m driftlessmap
+```
+
+```python
+import driftlessmap
+
+driftlessmap.run()
+```
+
+For an editable development install, clone the repository and use
+`python -m pip install -e .`.
+
+### Zeiss CZI files
+
+CZI support uses the optional `aicspylibczi` package, whose prebuilt packages
+currently support Python through 3.13:
+
+```bash
+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]"
+```
+
+## 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](MANUAL.md) for installation, atlas,
+registration, reconstruction, persistence, export, and troubleshooting
+guidance. The original [HERBS Cookbook](CookBook.pdf) and [tutorials](Tutorial)
+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.
+
+<img src="./driftlessmap/herbs.png" width="800px" alt="Historical HERBS interface used as the basis for DriftlessMap">
+
+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](WhatsNew.md) 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](LICENSE.txt) and
+[ORIGINS.md](ORIGINS.md).
+
+Please report issues or start discussions at
+<https://github.com/mohebi-n-associates/DriftlessMap>.

driftlessmap-1.1.0/README.md

@@ -0,0 +1,131 @@
+# 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](https://github.com/Whitlock-Group/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](LICENSE.txt), [project history](ORIGINS.md),
+[contributors](CONTRIBUTORS.md), [authors](AUTHOR.txt), and
+[acknowledgements](THANKS.txt).
+
+Current development is led by
+[Mohebi & Associates](https://www.mohebi-associates.org/), with
+[Ali Mohebi](https://www.mohebial.com/) 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](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.
+- 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.
+
+## Install
+
+DriftlessMap 1.1.0 supports Python 3.10–3.14 and Qt 6 through PyQt6. Python
+3.14 in a dedicated environment is recommended for new installations.
+
+```bash
+conda create --name DriftlessMap python=3.14 -y
+conda activate DriftlessMap
+python -m pip install --upgrade pip
+python -m pip install driftlessmap
+```
+
+Launch the application with any of:
+
+```bash
+driftlessmap
+python -m driftlessmap
+```
+
+```python
+import driftlessmap
+
+driftlessmap.run()
+```
+
+For an editable development install, clone the repository and use
+`python -m pip install -e .`.
+
+### Zeiss CZI files
+
+CZI support uses the optional `aicspylibczi` package, whose prebuilt packages
+currently support Python through 3.13:
+
+```bash
+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]"
+```
+
+## 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](MANUAL.md) for installation, atlas,
+registration, reconstruction, persistence, export, and troubleshooting
+guidance. The original [HERBS Cookbook](CookBook.pdf) and [tutorials](Tutorial)
+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.
+
+<img src="./driftlessmap/herbs.png" width="800px" alt="Historical HERBS interface used as the basis for DriftlessMap">
+
+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](WhatsNew.md) 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](LICENSE.txt) and
+[ORIGINS.md](ORIGINS.md).
+
+Please report issues or start discussions at
+<https://github.com/mohebi-n-associates/DriftlessMap>.

driftlessmap-1.1.0/THANKS.txt

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+DriftlessMap gratefully acknowledges everyone who created, tested, documented,
+and supported the original HERBS project. The original acknowledgements are
+preserved below.
+
+Dr. Menno P. Witter for providing anatomical support.
+
+Dr. Grethe M. Olsen for histological image data sharing and data registration confirmation anatomically contributions.
+
+Ida Välikangas Rautio for HERBS testing and histological image data sharing.
+
+Pearl Saldanha for testing and cookbook writing.
+
+Kristian Moan for light sheet data sharing and discussion.
+
+Paulo Jorge Bettencourt Girão for ideas and technical information on all types of microscopy.
+
+Abraham Z. Vollan for NP2.0 histological image data sharing and anatomical information providing.
+
+Dr. Jerneja Rudolf for HERBS testing.
+
+Dr. Noam Almog for HERBS testing.
+
+Dr. Jonathan R. Whitlock for administration and coordination.
+
+
+Institutions
+------------
+