driftlessmap 1.1.0__py3-none-any.whl

driftlessmap-1.1.0.dist-info/METADATA

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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>.

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+driftlessmap-1.1.0.dist-info/WHEEL,sha256=K260EYznzXsJYBQGqmI8VTxEdiZYNvDZwW9cBh9-_MA,91
+driftlessmap-1.1.0.dist-info/entry_points.txt,sha256=mz-FiGvAf75wJRwExaSPjv1xYJqLjG1xd2cmZU60oLs,50
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+driftlessmap-1.1.0.dist-info/RECORD,,

driftlessmap-1.1.0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (83.0.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

driftlessmap-1.1.0.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+driftlessmap = driftlessmap:run

driftlessmap-1.1.0.dist-info/licenses/LICENSE.txt

@@ -0,0 +1,23 @@
+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.dist-info/top_level.txt

@@ -0,0 +1 @@
+driftlessmap